Histone deacetylase inhibitors

ABSTRACT

Histone deacetylase is a metallo-enzyme with zinc at the active site. Compounds having a zinc-binding moiety, such as, for example, a hydroxamic acid group or a carboxylic acid group, can inhibit histone deacetylase. Histone deacetylase inhibition can repress gene expression, including expression of genes related to tumor suppression. Accordingly, inhibition of histone deacetylase can provide an alternate route for treating cancer, hematological disorders, e.g., hemoglobinopathies, genetic disorders, e.g. Huntington&#39;s disease and spinal muscular atrophy and genetic related metabolic disorders, e.g., cystic fibrosis and adrenoleukodystrophy.

CLAIM OF PRIORITY

This application is a divisional of, and claims priority to, U.S. patent application Ser. No. 11/489,519, filed Jul. 20, 2006, which is a continuation-in-part of U.S. patent application Ser. No. 09/812,945, filed Mar. 27, 2001, and a continuation-in-part of U.S. patent application Ser. No. 11/059,377, filed Feb. 17, 2005, which is a divisional of U.S. patent application Ser. No. 09/812,944, filed Mar. 27, 2001, now U.S. Pat. No. 6,495,719, each of which is incorporated by reference in its entirety.

This application is also a continuation of U.S. patent application Ser. No. 10/442,191, filed May 21, 2003, which claims priority to U.S. Patent Application No. 60/382,077, filed May 22, 2002, a continuation of U.S. patent application Ser. No. 10/442,175, filed May 21, 2003, which claims priority to U.S. Patent Application No. 60/382,075, filed May 22, 2002, and a continuation of U.S. patent application Ser. No. 11/198,293, filed Aug. 8, 2005, which is a divisional of U.S. patent application Ser. No. 10/442,177, filed May 21, 2003, now U.S. Pat. No. 7,057,057, which claims priority to U.S. Patent Application No. 60/382,089, filed May 22, 2002, each of which is incorporated by reference in its entirety.

TECHNICAL FIELD

This invention relates to enzyme inhibitors, and more particularly to histone deacetylase inhibitors.

BACKGROUND

DNA in the nucleus of the cell exists as a hierarchy of compacted chromatin structures. The basic repeating unit in chromatin is the nucleosome. The nucleosome consists of a histone octamer of proteins in the nucleus of the cell around which DNA is twice wrapped. The orderly packaging of DNA in the nucleus plays an important role in the functional aspects of gene regulation. Covalent modifications of the histones have a key role in altering chromatin higher order structure and function and ultimately gene expression. The covalent modification of histones, such as acetylation, occurs by enzymatically mediated processes.

Regulation of gene expression through the inhibition of the nuclear enzyme histone deacetylase (HDAC) is one of several possible regulatory mechanisms whereby chromatin activity can be affected. The dynamic homeostasis of the nuclear acetylation of histones can be regulated by the opposing activity of the enzymes histone acetyl transferase (HAT) and histone deacetylase (HDAC). Transcriptionally silent chromatin can be characterized by nucleosomes with low levels of acetylated histones. Acetylation of histones reduces the positive charge of histones, thereby expanding the structure of the nucleosome and facilitating the interaction of transcription factors with the DNA. Removal of the acetyl group restores the positive charge condensing the structure of the nucleosome. Histone acetylation can activate DNA transcription, enhancing gene expression. Histone deacetylase can reverse the process and can serve to repress gene expression. See, for example, Grunstein, Nature 389, 349-352 (1997); Pazin et al., Cell 89, 325-328 (1997); Wade et al., Trends Biochem. Sci. 22, 128-132 (1997); and Wolffe, Science 272, 371-372 (1996).

SUMMARY

Histone deacetylase is a metallo-enzyme with zinc at the active site. Compounds having a zinc-binding moiety, such as, for example, a hydroxamic acid group or a carboxylic acid group, can inhibit histone deacetylase. Histone deacetylase inhibition can alter gene expression, including expression of genes related to tumor suppression. Accordingly, inhibition of histone deacetylase can provide an alternate route for treating cancer, hematological disorders, e.g., hemoglobinopathies, genetic disorders, e.g. Huntington's disease, and spinal muscular atrophy and genetic related metabolic disorders, e.g., cystic fibrosis and adrenoleukodystrophy.

In one aspect, a method of treating spinal muscular atrophy in a mammal includes administering to the mammal an effective amount of an inhibitor of histone deacetylase. In one aspect, a method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound of formula (I), thereby treating one or more disorders mediated by histone deacetylase, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. The method can treat spinal muscular atrophy in a mammal by administering to the mammal an effective amount of a compound of formula (I).

The compound of formula (I) can be the following:

A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 4-14 membered heterocycloalkenyl, aryl, or heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; or A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; each of the saturated and the unsaturated branched hydrocarbon chain being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond, and each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. L is a straight C₂₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond; said hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. X¹ is O or S. X² is —OR¹, —SR¹, —NR³—OR¹, —NR³—SR¹, —C(O)—OR¹, —CHR⁴—OR¹, —N═N—C(O)—N(R³)₂, or —O—CHR⁴—O—C(O)—R⁵, where each of R¹ and R², independently, is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group, R³ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group, R⁴ is hydrogen, alkyl, hydroxylalkyl, or haloalkyl, and R⁵ is alkyl, hydroxylalkyl, or haloalkyl. When L is a C₂₋₃ hydrocarbon containing no double bonds and X² is —OR¹, Y¹ is not a bond and Y² is not a bond.

In another aspect, a method of inhibiting histone deacetylase in cells comprising contacting the cells with an effective amount of a compound of formula (I), supra, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. A is phenyl optionally substituted with alkyl alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, or amino. Each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, or a bond; where R^(c) is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. L is a straight C₂₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond, the hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—, and each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. X¹ is O or S. X² is —OR¹, —SR¹, —NR³—OR¹, —NR³—SR¹, —C(O)—OR¹, —CHR⁴—OR¹, —N═N—C(O)—N(R³)₂, or —O—CHR⁴—O—C(O)—R⁵, where each of R¹ and R², independently, is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group, R³ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group, R⁴ is hydrogen, alkyl, hydroxylalkyl, or haloalkyl, and R⁵ is alkyl, hydroxylalkyl, or haloalkyl. When L is a C₂₋₃ hydrocarbon containing no double bonds and X² is —OR¹, Y¹ is not a bond and Y² is not a bond.

In yet another aspect, a method of treating a histone deacetylase-mediated disorder includes administering to a subject in need thereof a therapeutically effective amount of compound of formula (I), supra.

In certain embodiments, X² can be —OR¹, —NR³—OR¹, —C(O)—OR¹, —CHR⁴—OR¹, or —O—CHR⁴—O—C(O)—R⁵, X² can be —OR¹, —NR³—OR¹, —C(O)OR¹, or —O—CHR⁴—O—C(O)—R⁵, each of Y¹ and Y², independently, can be —CH₂—, —O—, —N(R^(c))—, or a bond, L can be a saturated hydrocarbon chain, such as a C₃₋₈ hydrocarbon chain substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂.

In other embodiments, L can be an unsaturated hydrocarbon chain containing at least one double bond and no triple bond, such as an unsaturated C₄₋₈ hydrocarbon chain substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂. In other embodiments, L can be an unsaturated hydrocarbon chain containing at least one double bond and one triple bond, such as an unsaturated C₄₋₈ hydrocarbon chain substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂. The double bond can be in trans configuration.

In certain embodiments, A can be a C₅₋₈ cycloalkenyl or 5-8 membered heteroalkenyl containing at least one double bond. A can be phenyl, naphthyl, indanyl, or tetrahydronaphthyl, or A can be phenyl optionally substituted with alkyl alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, or amino. In other embodiments, A can contain only double bonds.

Set forth below are some examples of a compound that can be employed: 5-phenyl-2,4-pentadienoic acid, 3-methyl-5-phenyl-2,4-pentadienoic acid, 4-methyl-5-phenyl-2,4-pentadienoic acid, 4-chloro-5-phenyl-2,4-pentadienoic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoic acid, 5-(2-furyl)-2,4-pentadienoic acid, 5-phenyl-2-en-4-yn-pentanoic acid, 6-phenyl-3,5-hexadienoic acid, 7-phenyl-2,4,6-heptatrienoic acid, 8-phenyl-3,5,7-octatrienoic acid, potassium 2-oxo-6-phenyl-3,5-hexadienoate, potassium 2-oxo-8-phenyl-3,5,7-octatrienoate, cinnamoylhydroxamic acid, methyl-cinnamoylhydroxamic acid, 4-cyclohexanebutyroylhydroxamic acid, benzylthioglycoloylhydroxamic acid, 5-phenylpentanoylhydroxamic acid, 5-phenyl-2,4-pentadienoylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoylhydroxamic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid, 5-phenyl-2-en-4-yn-pentanoylhydroxamic acid, 5-(2-furyl)-2,4-pentadienoylhydroxamic acid, 6-phenylhexanoylhydroxamic acid, 6-phenyl-3,5-hexadienoylhydroxamic acid, N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid, 7-phenylheptanoylhydroxamic acid, 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid or 8-phenyloctanoylhydroxamic acid.

In another aspect, a method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound of formula (II), thereby treating one or more disorders mediated by histone deacetylase, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. The method can treat spinal muscular atrophy in a mammal In one aspect, hydroxamic acid-containing compounds have a structure of formula (II). In aspect, a compound has a formula (II).

A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-14 membered heterocycloalkenyl (e.g., C₃₋₈ cycloalkyl, 3-8 membered heterocycloalkyl, C₄₋₈ cycloalkenyl, 3-8 membered heterocycloalkenyl), monocyclic aryl, or monocyclic heteroaryl. Each of these cyclic moieties is optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylcarbonylamino, aminocarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Each of X¹ and X², independently, is O or S. Y¹ is —CH₂—, —O—, —S—, —N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—C(O)—O—, or a bond wherein each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Y² is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O— wherein each of R^(c) and R^(d), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. L is (1) a saturated straight C₁₋₁₂ hydrocarbon chain substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, halo, carboxyl, amino, nitro, cyano, C₃₋₆ cycloalkyl, 3-6 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, formyl, C₁₋₄ alkylcarbonylamino, or C₁₋₄ aminocarbonyl, or at least two hydroxyl; and further optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O— wherein each of R^(e) and R^(f), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; or L is (2) an unsaturated straight C₄₋₁₂ hydrocarbon chain containing at least two double bonds, at least one triple bond, or at least one double bond and one triple bond, where the unsaturated hydrocarbon chain is optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, carboxyl, amino, nitro, cyano, C₃₋₆ cycloalkyl, 3-6 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, formyl, C₁₋₄ alkylcarbonylamino, or C₁₋₄ aminocarbonyl; and further being optionally interrupted by —O—, —N(R^(g))—, —N(R^(g))—C(O)—O—, —O—C(O)—N(R^(g))—, —N(R^(g))—C(O)—N(R^(h))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O— wherein each of R^(g) and R^(h), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group; and R² is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group.

In another aspect, hydroxamic acid-containing compounds have a structure of formula (II), supra. A is a cyclic moiety selected from the group consisting of monocyclic aryl or monocyclic heteroaryl. Each of the cyclic moieties is optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, or amino. Each of X¹ and X², independently, is O or S. Y¹ is —CH₂—, —O—, —S—, —N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—C(O)—O—, or a bond, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Y² is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. L is (1) a saturated straight C₃₋₁₀ hydrocarbon chain substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, or amino, and further optionally interrupted by —O— or —N(R^(e))—, where R^(e) is hydrogen, alkyl, hydroxylalkyl, or haloalkyl; or L is (2) an unsaturated straight C₄₋₁₀ hydrocarbon chain containing at least two double bonds, at least one triple bond, or at least one double bond and one triple bond; said unsaturated hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, or amino, and further optionally interrupted by —O— or —N(R^(f))—, where R^(f) is hydrogen, alkyl, hydroxylalkyl, or haloalkyl. Each of R¹ and R², independently, is hydrogen, alkyl, hydroxylalkyl, or haloalkyl.

In certain embodiments, R¹ is hydrogen, R² is hydrogen, X¹ is O, X² is O, or Y¹ is —CH₂—, —O—, —N(R^(a))—, or a bond, and Y² is —CH₂—, —O—, or —N(R^(c))—. L can be a saturated straight C₄₋₁₀ hydrocarbon chain, or C₅₋₈ hydrocarbon chain (e.g., a saturated straight C₅ hydrocarbon chain, a saturated straight C₆ hydrocarbon chain, or a saturated straight C₇ hydrocarbon chain), substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, or amino, and further optionally interrupted by —O— or —N(R^(c))—. In other embodiments, L is an unsaturated straight C₄₋₁₀ hydrocarbon chain, or an unsaturated straight C₄₋₈ hydrocarbon chain, containing 2-5 double bonds, or 1-2 double bonds and 1-2 triple bonds, optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, or C₁₋₄ alkoxy, and further being optionally interrupted by —O— or —N(R^(g))—. In certain embodiments, L can be —(CH═CH)_(m)— where m is 2 or 3 or L can be —C≡C—(CH═CH)_(n)— where n is 1 or 2. A can be phenyl, furyl, thienyl, pyrrolyl, or pyridyl or A can be phenyl optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, or amino.

In a further aspect, hydroxamic acid-containing compounds have a structure of formula (III):

A is a cyclic moiety selected from the group consisting of monocyclic aryl or monocyclic heteroaryl. Each of the cyclic moieties is optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, or amino. Each of X¹ and X², independently, is O or S. Each of R¹ and R², independently, is hydrogen, alkyl, hydroxylalkyl, or haloalkyl. Each of R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹ and R¹⁰, independently, is hydrogen, C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, hydroxylC_(h4) alkyl, haloC₁₋₄ alkyl, or amino, and each of a, b, c, d, e, and f, independently, is 0 or 1. Note that at least one of b, c, d, and e cannot be zero. In certain embodiments, a is 0, f is 0, or the total number of b, c, d, and e is 3 or 4. In other embodiments, each of R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, and R¹⁰, independently, is hydrogen, C₁₋₄ alkyl, C₁₋₄ alkoxy, hydroxyl, hydroxylC₁₋₄ alkyl, or amino. Each of R⁵, R⁶, R⁷, and R⁸, independently can be hydrogen, C₁₋₄ alkyl, C₁₋₄ alkoxy, hydroxyl, hydroxylC₁₋₄ alkyl, or amino, Each of R³, R⁴, R⁹ and R¹⁰, independently, can be hydrogen.

In another aspect hydroxamic acid-containing compounds have the structure of formula (II), supra. A is a saturated branched C₃₋₁₄ hydrocarbon chain or an unsaturated branched C₃₋₁₄ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—C(O)—, —C(O)—N(R^(a))—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Each of the saturated and the unsaturated branched hydrocarbon chain is optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylcarbonylamino, aminocarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Each of X¹ and X², independently, is O or S. Each of Y¹ and Y², independently, is —CH₂—, —O—, —N(R^(c)), —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—, —C(O)—O—, —O—C(O)—O—, or a bond, where each of R^(c) and R^(d), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. L is a saturated straight C₃₋₁₂ hydrocarbon or an unsaturated straight C₄₋₁₂ hydrocarbon chain, said hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, carboxyl, amino, nitro, cyano, C₃₋₆ cycloalkyl, 3-6 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, formyl, C₁₋₄ alkylcarbonylamino, or C₁₋₄ aminocarbonyl; and further optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—, where each of R^(e) and R^(f), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group; and R² is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group.

Set forth below are some examples of a hydroxamic acid-containing compounds: benzylthioglycoloylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoylhydroxamic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid, 5-phenyl-2-en-4-yn-pentanoylhydroxamic acid, 5-(2-furyl)-2,4-pentadienoylhydroxamic acid, N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid, and 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid.

In another aspect, a method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound of formula (IV), thereby treating one or more disorders mediated by histone deacetylase, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. The method can treat spinal muscular atrophy in a mammal by administering to the mammal an effective amount of a compound of formula (IV). In one aspect, a compound has the formula (IV).

In formula (IV), A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, or heteroaryl. The cyclic moiety can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Alternatively, A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—. Each of R^(a) and R^(b), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Each of the saturated and the unsaturated branched hydrocarbon chain can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl.

In formula (IV), each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond. Each of R^(c) and R^(d), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In formula (IV), L is a straight C₃₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond. The hydrocarbon chain can be optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—. Each of R^(e) and R^(f), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. In formula (IV), X¹ is O or S and X² is —OR¹, —SR¹, or —SeR¹. R¹ can be hydrogen, alkyl, acyl, aryl or aralkyl. Preferably, X¹ is O, X² is —SR¹, R¹ is hydrogen, C₁₋₄ alkyl, or C₁₋₄ acyl, or combinations thereof.

In formula (IV), when Y¹ is a bond and L is saturated, the carbon adjacent to Y¹ is not substituted with C₁₋₄ alkoxy or hydroxyl.

In formula (IV), in certain circumstances, A is phenyl, Y¹ is a bond, and L is a C₆₋₁₂ hydrocarbon chain containing three double bonds and the carbon adjacent to Y¹ is substituted with phenyl. In other circumstances, A is phenyl, Y¹ is a bond, and L is a C₃₋₁₂ hydrocarbon chain and the carbon adjacent to Y¹ is substituted with two phenyls.

In another aspect, a compound has formula (V):

In formula (V), A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, or heteroaryl. The cyclic moiety can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl.

In formula (V), L is a straight C₂₋₁₂ hydrocarbon chain containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond. The hydrocarbon chain can be optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—. Each of R^(a) and R^(b), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; and being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl.

In formula (V), X¹ is O or S and X² is —OR¹, or —SR¹. R¹ can be hydrogen, alkyl, acyl, aryl or aralkyl. Preferably, X¹ is O, X² is —SR¹, R¹ is hydrogen, C₁₋₄ alkyl, or C₁₋₄ acyl, or combinations thereof

In formula (V), when L is a C₂ hydrocarbon chain having at least one double bond, A is not C₃ cycloalkyl.

The compound can be S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate or S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate.

In another aspect, a method of inhibiting histone deacetylation activity in cells. The method includes contacting the cells with an effective amount of a compound of formula (IV), thereby treating one or more disorders mediated by histone deacetylase or stimulating hematopoietic cells ex vivo, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. When used in the method, the compound is of formula (IV)

In the method, A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, or heteroaryl. The cyclic moiety can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Alternatively, A is a saturated C₁₋₁₂ hydrocarbon chain or an unsaturated C₂₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—. Each of R^(a) and R^(b), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Each of the saturated and the unsaturated branched hydrocarbon chain can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl.

In the method, each of Y¹ and Y², independently, can be —CH₂—, —O—, —S—, —N(R^(c))—, —C(O)—, —C(NOR^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond. Each of R^(c) and R^(d), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In the method, L is a straight C₁₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond. The hydrocarbon chain can be optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl. The hydrocarbon chain can be optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—. Each of R^(e) and R^(f), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In the method, X¹ is O or S and X² is —OR¹, —SR¹, or —SeR¹. R¹ can be hydrogen, alkyl, acyl, aryl or aralkyl. Preferably, X¹ is O, X² is —SR¹, R¹ is hydrogen or C₁₋₄ acyl, or combinations thereof.

In the method, when Y¹ is a bond and L is saturated, the carbon adjacent to Y¹ is not substituted with C₁₋₄ alkoxy or hydroxyl and when Y¹ is —C(O)—, —C(NOR^(c))—, L is not saturated.

In the method, the compound can be ethylene glycol bisthioglycolate, S-(2-oxo-4-phenyl)butyl thioacetate, ethyl 2-mercaptoacetate, S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate, or S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate.

The disorder can be cancer, hemoglobinopathies, thalassemia, sickle cell anemia, cystic fibrosis, protozoan infection, spinal muscular atrophy, Huntington's disease, alpha-1 anti-trypsin, retrovirus gene vector reactivation, wound healing, hair growth, peroxisome biogenesis disorder, or adrenoleukodystrophy.

In certain circumstances, Y¹ can be not a bond and L can be a C₃₋₈ hydrocarbon chain optionally substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂. In other circumstances, each of Y¹ and Y², independently, can be —CH₂—, —O—, —N(R^(c))—, or a bond.

In certain circumstances, L can be a C₃₋₈ hydrocarbon chain, a C₄₋₁₂ hydrocarbon chain, a C₅₋₁₂ hydrocarbon chain, a C₅₋₁₀ hydrocarbon chain, or a C₆₋₈ hydrocarbon chain. L can be substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂. L can be an unsaturated hydrocarbon chain containing at least one double bond or at least two double bonds. The double bond can be in trans configuration.

In certain circumstances, A can be a C₅₋₈ cycloalkenyl, 5-8 membered heteroalkenyl, phenyl, naphthyl, indanyl, or tetrahydronaphthyl. A can be optionally substituted with alkyl alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, or amino.

In another aspect, a method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound of formula (VI), thereby treating one or more disorders mediated by histone deacetylase, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. The method can treat spinal muscular atrophy in a mammal. In one aspect, hydroxamic acid-containing compounds have a structure of formula (VI).

In another aspect, method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound containing a trihalomethylcarbonyl group, thereby treating one or more disorders mediated by histone deacetylase or stimulating hematopoietic cells ex vivo, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. The compound can be of formula (VI). In the method, the compound can be 1,1,1-trifluoro-5-phenyl-2-pentanone, 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one, or 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one. The disorder can be cancer, hemoglobinopathies, thalassemia, sickle cell anemia, cystic fibrosis, protozoan infection, spinal muscular atrophy, Huntington's disease, alpha-1 anti-trypsin, retrovirus gene vector reactivation, wound healing, hair growth, peroxisome biogenesis disorder, or adrenoleukodystrophy.

In formula (VI), A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, or heteroaryl. The cyclic moiety is optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Alternatively, A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—. Each of R^(a) and R^(b), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Each of the saturated and the unsaturated branched hydrocarbon chain is optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl.

In formula (VI), each of Y¹ and Y², independently, is —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond. Each of R^(c) and R^(d), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In formula (VI), L is a straight C₃₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond. The hydrocarbon chain can be optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl. The hydrocarbon chain can be optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—. Each of R^(e) and R^(f), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In formula (VI), X¹ is O or S.

In formula (VI), X² is a halogen.

In formula (VI), when Y¹ and Y² are each a bond, L is a C₆₋₁₂ hydrocarbon chain containing at least one double bond at C1, C2, C3 or C5 of the hydrocarbon chain from C═X¹, at least one triple bond, or at least one double bond and one triple bond.

In certain circumstances: X² can be fluorine; Y¹ can be not a bond; each of Y¹ and Y², independently, can be —O—, —N(R^(c)), or a bond; X¹ can be O; L can be a C₆₋₈ hydrocarbon chain substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂; L can be a C₄₋₁₂ hydrocarbon chain; L can be a C₅₋₁₂ hydrocarbon chain; L can be a C₅₋₁₀ hydrocarbon chain, L can be an unsaturated hydrocarbon chain containing at least two double bonds; or A can be a C₅₋₈ cycloalkenyl, 5-8 membered heteroalkenyl, phenyl, naphthyl, indanyl, or tetrahydronaphthyl optionally substituted with alkyl alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, or amino.

In certain circumstances, A is phenyl, Y¹ is a bond, and L is a C₆₋₁₂ hydrocarbon chain containing three double bonds and the carbon adjacent to Y¹ is substituted with phenyl. In other circumstances, A is phenyl, Y¹ is a bond, and L is a C₃₋₁₂ hydrocarbon chain and the carbon adjacent to Y¹ is substituted with two phenyls.

In formula (VI), the compound can be 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one or 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one.

In another aspect, a method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound of formula (VII), thereby treating one or more disorders mediated by histone deacetylase, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. The method can treat spinal muscular atrophy in a mammal. In one aspect, a method of inhibiting histone deacetylation activity in cells includes contacting the cells with an effective amount of a compound containing an alpha-ketoepoxide group, wherein the compound is not trapoxin, thereby treating one or more disorders mediated by histone deacetylase to stimulate hematopoietic cells ex vivo, and determining whether the level of acetylated histones in the treated cells is higher than in untreated cells under the same conditions. In the method, the compound can be a compound of formula (VII), provided that when each of Y¹ and Y², independently, is a bond or CH₂, A is unsubstituted phenyl or heterocyclyl, and L is C₄₋₆, L has at least one double bond or at least one triple bond. In the method, the compound can be 1-oxiranyl-8-phenyl-1-octanone, 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one, or 1-oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one.

A compound has the formula (VII):

In formula (VII), A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, or heteroaryl. The cyclic moiety can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl. Alternatively, A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—. Each of R^(a) and R^(b), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl. Each of the saturated and the unsaturated branched hydrocarbon chain can be optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl.

In formula (VII), each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —C(O)—, —C(NR^(c))—, —O—C(O)—O—, or a bond. Each of R^(c) and R^(d), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In formula (VII), L is a straight C₄₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond. The hydrocarbon chain can be optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl. The hydrocarbon chain can be optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—. Each of R^(e) and R^(f), independently, can be hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl.

In formula (VII), X¹ is O or S, and each of R^(g), R^(h), and R^(i), independently, is hydrogen or C₁₋₆ alkyl.

In formula (VII), when each of Y¹ and Y², independently, is a bond or CH₂, A is unsubstituted phenyl or heterocyclyl, and L is C₄₋₇, L has at least one double bond or at least one triple bond. In formula (VII), when each of Y¹ and Y² is a bond, A is unsubstituted phenyl, and L is C₄, L is not a diene.

In certain circumstances: each of R^(g), R^(h), and R^(i) can be hydrogen; X¹ can be O; each of Y¹ and Y², independently, can be —CH₂—, —O—, —N(R^(c))—, or a bond; L can be a C₄₋₁₂ hydrocarbon chain, a C₅₋₁₂ hydrocarbon chain, a C₅₋₁₀ hydrocarbon chain, or a C₆₋₈ hydrocarbon chain; L can be optionally substituted with C₁₋₂ alkyl, C₁₋₂ alkoxy, hydroxyl, —NH₂, —NH(C₁₋₂ alkyl), or —N(C₁₋₂ alkyl)₂; L can contain at least one double bond, at least one triple bond, or at least one double bond and one triple bond; L can be an unsaturated hydrocarbon chain containing at least one double bond; the double bond can be in trans configuration; L can be an unsaturated hydrocarbon chain containing at least two double bonds; or A is a C₅₋₈ cycloalkenyl, 5-8 membered heteroalkenyl, phenyl, naphthyl, indanyl, or tetrahydronaphthyl optionally substituted with alkyl alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, or amino.

In formula (VII), the compound can be 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one, or 1-oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one.

In one aspect, a method of treating spinal muscular atrophy in a mammal includes administering to the mammal an effective amount of an inhibitor of histone deacetylase selected from the group consisting of: 5-phenyl-2,4-pentadienoic acid, 3-methyl-5-phenyl-2,4-pentadienoic acid, 4-methyl-5-phenyl-2,4-pentadienoic acid, 4-chloro-5-phenyl-2,4-pentadienoic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoic acid, 5-(2-furyl)-2,4-pentadienoic acid, 5-phenyl-2-en-4-yn-pentanoic acid, 6-phenyl-3,5-hexadienoic acid, 7-phenyl-2,4,6-heptatrienoic acid, 8-phenyl-3,5,7-octatrienoic acid, potassium 2-oxo-6-phenyl-3,5-hexadienoate, potassium 2-oxo-8-phenyl-3,5,7-octatrienoate, cinnamoylhydroxamic acid, methyl-cinnamoylhydroxamic acid, 4-cyclohexanebutyroylhydroxamic acid, benzylthioglycoloylhydroxamic acid, 5-phenylpentanoylhydroxamic acid, 5-phenyl-2,4-pentadienoylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoylhydroxamic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid, 5-phenyl-2-en-4-yn-pentanoylhydroxamic acid, 5-(2-furyl)-2,4-pentadienoylhydroxamic acid, 6-phenylhexanoylhydroxamic acid, 6-phenyl-3,5-hexadienoylhydroxamic acid, N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid, 7-phenylheptanoylhydroxamic acid, 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid, 8-phenyloctanoylhydroxamic acid, benzylthioglycoloylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoyl hydroxamic acid, S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate, S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate, 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one or 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one, 1-oxiranyl-8-phenyl-1-octanone, 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one, and 1-oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one.

In one aspect, method of treating spinal muscular atrophy in a mammal comprising administering to the mammal an effective amount of 7-phenyl-2,4,6-heptatrienoic acid.

In certain circumstances, A is phenyl, Y¹ is a bond, and L is a C₆₋₁₂ hydrocarbon chain containing three double bonds and the carbon adjacent to Y¹ is substituted with phenyl. In other circumstances, A is phenyl, Y¹ is a bond, and L is a C₃₋₁₂ hydrocarbon chain and the carbon adjacent to Y¹ is substituted with two phenyls.

A salt of any of the compounds described herein can be prepared. For example, a pharmaceutically acceptable salt can be formed when an amino-containing compound of this invention reacts with an inorganic or organic acid. Some examples of such an acid include hydrochloric acid, hydrobromic acid, hydroiodic acid, sulfuric acid, phosphoric acid, p-bromophenylsulfonic acid, carbonic acid, succinic acid, citric acid, benzoic acid, and acetic acid. Examples of pharmaceutically acceptable salts thus formed include sulfate, pyrosulfate bisulfate, sulfite, bisulfite, phosphate, monohydrogenphosphate, dihydrogenphosphate, metaphosphate, pyrophosphate, chloride, bromide, iodide, acetate, propionate, decanoate, caprylate, acrylate, formate, isobutyrate, caprate, heptanoate, propiolate, oxalate, malonate, succinate, suberate, sebacate, fumarate, and maleate. A compound of this invention may also form a pharmaceutically acceptable salt when a compound of this invention having an acid moiety reacts with an inorganic or organic base. Such salts include those derived from inorganic or organic bases, e.g., alkali metal salts such as sodium, potassium, or lithium salts; alkaline earth metal salts such as calcium or magnesium salts; or ammonium salts or salts of organic bases such as morpholine, piperidine, pyridine, dimethylamine, or diethylamine salts.

It should be recognized that a compound can contain chiral carbon atoms. In other words, it may have optical isomers or diastereoisomers.

Alkyl is a straight or branched hydrocarbon chain containing 1 to 10 (preferably, 1 to 6; more preferably 1 to 4) carbon atoms. Examples of alkyl include, but are not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, 2-methylhexyl, and 3-ethyloctyl.

The terms “alkenyl” and “alkynyl” refer to a straight or branched hydrocarbon chain containing 2 to 10 carbon atoms and one or more (preferably, 1-4 or more preferably 1-2) double or triple bonds, respectively. Some examples of alkenyl and alkynyl are allyl, 2-butenyl, 2-pentenyl, 2-hexenyl, 2-butynyl, 2-pentynyl, and 2-hexynyl.

Cycloalkyl is a monocyclic, bicyclic or tricyclic alkyl group containing 3 to 14 carbon atoms. Some examples of cycloalkyl are cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, and norbornyl. Heterocycloalkyl is a cycloalkyl group containing at least one heteroatom (e.g., 1-3) such as nitrogen, oxygen, or sulfur. The nitrogen or sulfur may optionally be oxidized and the nitrogen may optionally be quaternized. Examples of heterocycloalkyl include piperidinyl, piperazinyl, tetrahydropyranyl, tetrahydrofuryl, and morpholinyl. Cycloalkenyl is a cycloalkyl group containing at least one (e.g., 1-3) double bond. Examples of such a group include cyclopentenyl, 1,4-cyclohexa-di-enyl, cycloheptenyl, and cyclooctenyl groups. By the same token, heterocycloalkenyl is a cycloalkenyl group containing at least one heteroatom selected from the group of oxygen, nitrogen or sulfur.

Aryl is an aromatic group containing a 5-14 member ring and can contain fused rings, which may be saturated, unsaturated, or aromatic. Examples of an aryl group include phenyl, naphthyl, biphenyl, phenanthryl, and anthracyl. If the aryl is specified as “monocyclic aryl,” if refers to an aromatic group containing only a single ring, i.e., not a fused ring.

Heteroaryl is aryl containing at least one (e.g., 1-3) heteroatom such as nitrogen, oxygen, or sulfur and can contain fused rings. Some examples of heteroaryl are pyridyl, furanyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, indolyl, benzofuranyl, and benzthiazolyl.

The cyclic moiety can be a fused ring formed from two or more of the just-mentioned groups. Examples of a cyclic moiety having fused rings include fluorenyl, dihydro-dibenzoazepine, dibenzocycloheptenyl, 7H-pyrazino[2,3-c]carbazole, or 9,10-dihydro-9,10-[2]buteno-anthracene.

Amino protecting groups and hydroxy protecting groups are well-known to those in the art. In general, the species of protecting group is not critical, provided that it is stable to the conditions of any subsequent reaction(s) on other positions of the compound and can be removed without adversely affecting the remainder of the molecule. In addition, a protecting group may be substituted for another after substantive synthetic transformations are complete. Examples of an amino protecting group include, but not limited to, carbamates such as 2,2,2-trichloroethylcarbamate or tertbutylcarbamate. Examples of a hydroxy protecting group include, but not limited to, ethers such as methyl, t-butyl, benzyl, p-methoxybenzyl, p-nitrobenzyl, allyl, trityl, methoxymethyl, 2-methoxypropyl, methoxyethoxymethyl, ethoxyethyl, tetrahydropyranyl, tetrahydrothiopyranyl, and trialkylsilyl ethers such as trimethylsilyl ether, triethylsilyl ether, dimethylarylsilyl ether, triisopropylsilyl ether and t-butyldimethylsilyl ether; esters such as benzoyl, acetyl, phenylacetyl, formyl, mono-, di-, and trihaloacetyl such as chloroacetyl, dichloroacetyl, trichloroacetyl, trifluoroacetyl; and carbonates including but not limited to alkyl carbonates having from one to six carbon atoms such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl; isobutyl, and n-pentyl; alkyl carbonates having from one to six carbon atoms and substituted with one or more halogen atoms such as 2,2,2-trichloroethoxymethyl and 2,2,2-trichloro-ethyl; alkenyl carbonates having from two to six carbon atoms such as vinyl and allyl; cycloalkyl carbonates having from three to six carbon atoms such as cyclopropyl, cyclobutyl, cyclopentyl and cyclohexyl; and phenyl or benzyl carbonates optionally substituted on the ring with one or more C₁₋₆ alkoxy, or nitro. Other protecting groups and reaction conditions can be found in T. W. Greene, Protective Groups in Organic Synthesis, (3rd, 1999, John Wiley & Sons, New York, N.Y.).

Note that an amino group can be unsubstituted (i.e., —NH₂), mono-substituted (i.e., —NHR), or di-substituted (i.e., —NR₂). It can be substituted with groups (R) such as alkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, aralkyl, or heteroaralkyl. Halo refers to fluoro, chloro, bromo, or iodo.

Inhibition of a histone deacetylase in a cell is determined by measuring the level of acetylated histones in the treated cells and measuring the level of acetylated histones in untreated cells and comparing the levels. If the level of histone acetylation in the treated cells increases relative to the untreated cells, histone deacetylase has been inhibited.

Some disorders or physiological conditions may be mediated by hyperactive histone deacetylase activity. A disorder or physiological condition that is mediated by histone deacetylase refers to a disorder or condition wherein histone deacetylase plays a role in triggering the onset thereof. Examples of such disorders or conditions include, but not limited to, cancer, hemoglobinopathies (e.g., thalassemia or sickle cell anemia), cystic fibrosis, protozoan infection, adrenoleukodystrophy, alpha-1 anti-trypsin, retrovirus gene vector reactivation, wound healing, hair growth, peroxisome biogenesis disorder, spinal muscular atrophy and adrenoleukodystrophy.

Other features or advantages will be apparent from the following detailed description of several embodiments, and also from the appended claims.

DETAILED DESCRIPTION

An aldehyde or carboxylic acid-containing compound can be prepared by any known methods in the art. For example, a compound having an unsaturated hydrocarbon chain between A and —C(═X¹)— can be prepared according to the following scheme A:

where L′ is a saturated or unsaturated hydrocarbon linker between A and —CH═CH— in a compound, and A and X¹ has the same meaning as defined above. See Coutrot et al., Syn. Comm. 133-134 (1978). Briefly, butyllithium can be added to an appropriate amount of anhydrous tetrahydrofuran (THF) at a very low temperature (e.g., −65° C.). A second solution having diethylphosphonoacetic acid in anhydrous THF can be added dropwise to the stirred butyllithium solution at the same low temperature. The resulting solution can be stirred at the same temperature for an additional 30-45 minutes which can be followed by the addition of a solution containing an aromatic acrylaldehyde in anhydrous THF over 1-2 hours. The reaction mixture can then warmed to room temperature and stirred overnight. It can then acidified (e.g., with HCl) which allows the organic phase to be separated. The organic phase can then dried, concentrated, and purified (e.g., by recrystallization) to form an unsaturated carboxylic acid-containing intermediate.

Alternatively, a carboxylic acid-containing compound can be prepared by reacting an acid ester of the formula A-L′—C(═O)—O-lower alkyl with a Grignard reagent (e.g., methyl magnesium iodide) and a phosphorus oxychloride to form a corresponding aldehyde, which can be further oxidized (e.g., by reacting with silver nitrate and aqueous NaOH) to form an unsaturated carboxylic acid-containing intermediate.

Other types of carboxylic acid-containing compounds (e.g., those containing a linker with multiple double bonds or triple bonds) can be prepared according to published procedures such as those described, for example, in Parameswara et al., Synthesis, 815-818 (1980) and Denny et al., J. Org. Chem., 27, 3404 (1962).

Carboxylic acid-containing compounds described above can then be converted to hydroxamic acid-containing compounds according to the following scheme B:

Triethylamine (TEA) is added to a cooled (e.g., 0-5° C.) anhydrous THF solution containing the carboxylic acid. Isobutyl chloroformate is then added to the solution having carboxylic acid, which is followed by the addition of hydroxylamine hydrochloride and TEA. After acidification, the solution was filtered to collect the desired hydroxamic acid-containing compounds.

An N-substituted hydroxamic acid can be prepared in a similar manner as described above. A corresponding carboxylic acid A-L′—C(═O)—OH can be converted to an acid chloride by reacting with oxalyl chloride (in appropriate solvents such as methylene chloride and dimethylformamide), which in turn, can be converted to a desired N-substituted hydroxamic acid by reacting the acid chloride with an N-substituted hydroxylamine hydrochloride (e.g., CH₃NHOH.HCl) in an alkaline medium (e.g., 40% NaOH (aq)) at a low temperature (e.g., 0-5° C.). The desired N-substituted hydroxamic acid can be collected after acidifying the reaction mixture after the reaction has completed (e.g., in 2-3 hours).

As to compounds wherein X¹ is S, they can be prepared according to procedures described in Sandler, S. R. and Karo, W., Organic Functional Group Preparations, Volume III (Academic Press, 1972) at pages 436-437. For preparation of compounds wherein X² is —N(R^(c))OH— and X¹ is S, see procedures described in U.S. Pat. Nos. 5,112,846; 5,075,330 and 4,981,865.

Compounds containing an α-keto acid moiety (e.g., when X¹ is oxygen and X² is —C(═O)OM or A-L′—C(═O)—C(═O)—OM, where A and L′ have been defined above and M can be hydrogen, lower alkyl or a cation such as K⁺), these compounds can be prepared by procedures based on that described in Schummer et al., Tetrahedron, 43, 9019 (1991). Briefly, the procedure starts with a corresponding aldehyde-containing compound (e.g., A-L′—C(═O)—H), which is allowed to react with a pyruvic acid in a basic condition (KOH/methanol) at a low temperature (e.g., 0-5° C.). Desired products (in the form of a potassium salt) are formed upon warming of the reaction mixture to room temperature.

The compounds described above, as well as their (thio)hydroxamic acid or α-keto acid counterparts, can possess histone deacetylase inhibitory properties.

The compounds of formula (IV) and (V) can generally be prepared according to the following methods. The alpha-chalcogenmethylcarbonyls can be prepared from a methyl ketone, as shown in Scheme C. Generally, a methyl ketone can be activated as a silyl enol ether. Next, the silyl enol ether can react with thionyl chloride to form a chloromethyl ketone. The chloromethyl ketone can then react with a chalcogen-containing compound of the formula X²H, where X² is —OR¹, —SR¹, or —SeR¹, and R¹ is hydrogen, alkyl, acyl, aryl or aralkyl. Alternatively, the alpha-chalcogenmethylcarbonyl can be made by converting a carboxylic acid to the corresponding chloromethyl ketone by sequential treatment with oxalyl chloride, diazomethane, and HCl, as summarized in Scheme D. The resulting chloromethyl ketone can then converted to the alpha-chalcogenmethylcarbonyl as shown in Scheme C.

The compounds of formula (VI) can generally be prepared according to the following methods. The trihalomethylcarbonyl compounds can be prepared from an aldehyde as shown in Scheme E. In particular, the trihalomethylcarbonyl compound can be prepared by reacting the aldehyde in THF with an equal amount of acetic acid and piperidine followed by addition of 1,1,1-trifluoroacetone at room temperature under nitrogen.

The carbon-carbon double bond can be selectively reduced or otherwise modified. The aldehyde can be prepared, for example, from a carboxylic acid-containing compound. These compound can be prepared by any method known in the art. For example, a compound having an unsaturated hydrocarbon chain between A and —C(═X¹)— can be prepared according to scheme A.

The compounds of formula (VII) can generally be prepared according to the following methods. Specifically, an alpha-ketoepoxide can be made by dropwise addition of sodium hydroxide to an aldehyde and 1,2-epoxy-3-butanone at a controlled pH of 8.5-9, as shown in Scheme F.

Alternatively, as shown in Scheme G, an alpha-ketoepoxide can be prepared by converting a carboxylic acid to the corresponding Weinreb amide using oxalyl chloride followed by N,O-dimethylhydroxylamine. Subsequently, the Weinreb amide is treated with vinyl Grignard. The resulting vinyl ketone is oxidized with, for example, with m-chloroperbenzoic acid (mCPBA) or an epoxidation catalyst such as Jacobsen's catalyst, to gives the desired alpha-ketoepoxide.

Note that appropriate protecting groups may be needed to avoid forming side products during the preparation of a compound. For example, if the linker L′ contains an amino substituent, it can be first protected by a suitable amino protecting group such as trifluoroacetyl or tert-butoxycarbonyl prior to being treated with reagents such as butyllithium. See, e.g., T. W. Greene, supra, for other suitable protecting groups.

A compound produced by the methods shown above can be purified by flash column chromatography, preparative high performance liquid chromatography, or crystallization.

A pharmaceutical composition including compounds described above can be used to inhibit histone deacetylase in cells and can be used to treat disorders associated with abnormal histone deacetylase activity. Some examples of these disorders are cancers (e.g., leukemia, lung cancer, colon cancer, CNS cancer, melanoma, ovarian cancer, cervical cancer, renal cancer, prostate cancer, and breast cancer), hematological disorders (e.g., hemoglobinopathies, thalassemia, and sickle cell anemia), genetic disorders (e.g. Huntington's disease and spinal muscular atrophy) and genetic related metabolic disorders (e.g., cystic fibrosis, peroxisome biogenesis disorder, alpha-1 anti-trypsin, and adrenoleukodystrophy). The compounds described above can also stimulate hematopoietic cells ex vivo, ameliorating protozoal parasitic infection, accelerate wound healing, and protecting hair follicles.

An effective amount is defined as the amount which is required to confer a therapeutic effect on the treated patient, and is typically determined based on age, surface area, weight, and condition of the patient. The interrelationship of dosages for animals and humans (based on milligrams per meter squared of body surface) is described by Freireich et al., Cancer Chemother. Rep. 50, 219 (1966). Body surface area may be approximately determined from height and weight of the patient. See, e.g., Scientific Tables, Geigy Pharmaceuticals, Ardsley, N.Y., 1970, 537. An effective amount of a compound described herein can range from about 1 mg/kg to about 300 mg/kg. Effective doses will also vary, as recognized by those skilled in the art, dependent on route of administration, excipient usage, and the possibility of co-usage, pre-treatment, or post-treatment, with other therapeutic treatments including use of other chemotherapeutic agents and radiation therapy. Other chemotherapeutic agents that can be co-administered (either simultaneously or sequentially) include, but not limited to, paclitaxel and its derivatives (e.g., taxotere), doxorubicin, L-asparaginase, dacarbazine, amascrine, procarbazine, hexamethylmelamine, mitoxantrone, and gemicitabine.

The pharmaceutical composition may be administered via the parenteral route, including orally, topically, subcutaneously, intraperitoneally, intramuscularly, and intravenously. Examples of parenteral dosage forms include aqueous solutions of the active agent, in a isotonic saline, 5% glucose or other well-known pharmaceutically acceptable excipient. Solubilizing agents such as cyclodextrins, or other solubilizing agents well-known to those familiar with the art, can be utilized as pharmaceutical excipients for delivery of the therapeutic compounds. Because some of the compounds described herein can have limited water solubility, a solubilizing agent can be included in the composition to improve the solubility of the compound. For example, the compounds can be solubilized in polyethoxylated castor oil (Cremophor EL®) and may further contain other solvents, e.g., ethanol. Furthermore, compounds described herein can also be entrapped in liposomes that may contain tumor-directing agents (e.g., monoclonal antibodies having affinity towards tumor cells).

A compound described herein can be formulated into dosage forms for other routes of administration utilizing conventional methods. For example, it can be formulated in a capsule, a gel seal, or a tablet for oral administration. Capsules may contain any standard pharmaceutically acceptable materials such as gelatin or cellulose. Tablets may be formulated in accordance with conventional procedures by compressing mixtures of a compound described herein with a solid carrier and a lubricant. Examples of solid carriers include starch and sugar bentonite. Compounds of this invention can also be administered in a form of a hard shell tablet or a capsule containing a binder, e.g., lactose or mannitol, a conventional filler, and a tableting agent.

The activities of a compound described herein can be evaluated by methods known in the art, e.g., MTT (3-[4,5-d]mehtythiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay, clonogenic assay, ATP assay, or Extreme Drug Resistance (EDR) assay. See Freuhauf, J. P. and Manetta, A., Chemosensitivity Testing in Gynecologic Malignancies and Breast Cancer 19, 39-52 (1994). The EDR assay, in particular, is useful for evaluating the antitumor and antiproliferative activity of a compound described herein (see Example 28). Cells are treated for four days with a compound. Both untreated and treated cells are pulsed with tritiated thymidine for 24 hours. Radioactivity of each type of cells is then measured and compared. The results are then plotted to generate drug response curves, which allow IC₅₀ values (the concentration of a compound required to inhibit 50% of the population of the treated cells) to be determined.

The histone acetylation activity of a compound described herein can be evaluated in an assay using mouse erythroleukemia cells. Studies are performed with the DS19 mouse erythroleukemia cells maintained in RPMI 1640 medium with 25 mM HEPES buffer and 5% fetal calf serum. The cells are incubated at 37° C.

Histones are isolated from cells after incubation for periods of 2 and 24 hours. The cells are centrifuged for 5 minutes at 2000 rpm in the Sorvall SS34 rotor and washed once with phosphate buffered saline. The pellets are suspended in 10 ml lysis buffer (10 mM Tris, 50 mM sodium bisulfite, 1% Triton X-100, 10 mM magnesium chloride, 8.6% sucrose, pH 6.5) and homogenized with six strokes of a Teflon pestle. The solution is centrifuged and the pellet washed once with 5 ml of the lysis buffer and once with 5 ml 10 mM Tris, 13 mM EDTA, pH 7.4. The pellets are extracted with 2×1 mL 0.25N HCl. Histones are precipitated from the combined extracts by the addition of 20 mL acetone and refrigeration overnight. The histones are pelleted by centrifuging at 5000 rpm for 20 minutes in the Sorvall SS34 rotor. The pellets are washed once with 5 mL acetone and protein concentrations are quantitated by the Bradford procedure.

Separation of acetylated histones is usually performed with an acetic acid-urea polyacrylamide gel electrophoresis procedure. Resolution of acetylated H4 histones is achieved with 6,25N urea and no detergent as originally described by Panyim and Chalkley, Arch. Biochem. Biophys. 130, 337-346, 1969. 25 μg total histones are applied to a slab gel which is run at 20 ma. The run is continued for a further two hours after the Pyronon Y tracking dye has run off the gel. The gel is stained with Coomassie Blue R. The most rapidly migrating protein band is the unacetylated H4 histone followed by bands with 1, 2, 3 and 4 acetyl groups which can be quantitated by densitometry. The procedure for densitometry involves digital recording using the Alpha Imager 2000, enlargement of the image using the PHOTOSHOP program (Adobe Corp.) on a MACINTOSH computer (Apple Corp.), creation of a hard copy using a laser printer and densitometry by reflectance using the Shimadzu CS9000U densitometer. The percentage of H4 histone in the various acetylated states is expressed as a percentage of the total H4 histone.

The concentration of a compound required to decrease the unacetylated H4 histone by 50% (i.e., EC₅₀) can then be determined from data obtained using different concentrations of test compounds.

Histone deacetylase inhibitory activity can be measured based on procedures described by Hoffmann et al., Nucleic Acids Res., 27, 2057-2058 (1999). See Example 30. Briefly, the assay starts with incubating the isolated histone deacetylase enzyme with a compound, followed by the addition of a fluorescent-labeled lysine substrate (contains an amino group at the side chain which is available for acetylation). HPLC is used to monitor the labeled substrate. The range of activity of each test compound is preliminarily determined using results obtained from HPLC analyses. IC₅₀ values can then be determined from HPLC results using different concentrations of compounds of this invention. All assays are duplicated or triplicated for accuracy. The histone deacetylase inhibitory activity can be compared with the increased activity of acetylated histone for confirmation.

Compounds of this invention are also evaluated for effects on treating X-linked adrenoleukodystrophy (X-ALD), a peroxisomal disorder with impaired very long-chain fatty acid (VLCFA) metabolism. In such an assay, cell lines derived from human primary fibroblasts and (EBV-transformed lymphocytes) derived from X-ALD patients grown in RPMI are employed. Tissue culture cells are grown in the presence or absence of test compounds. For VLCFA measurements, total lipids are extracted, converted to methyl esters, purified by TLC and subjected to capillary GC analysis as described in Moser et al., Technique in Diagnostic Biochemical Genetics: A Laboratory Manual (ed. A., H.F.) 177-191 (Wiley-Liss, New York, 1991). C24:0 β-oxidation activity of lymphoclastoid cells are determined by measuring their capacity to degrade [1-¹⁴C]—C24:0 fatty acid to water-soluble products as described in Watkins et al., Arch. Biochem. Biophys. 289, 329-336 (1991). The statistical significance of measured biochemical differences between untreated and treated X-ALD cells can be determined by a two-tailed Student's t-test. See Example 31.

Further, compounds described herein are evaluated for their effects in treating cystic fibrosis (CF). Since the initial defect in the majority of cases of CF is the inability of mutant CF protein (CFTR) to fold properly and exit the ER, compounds are tested to evaluate their efficacy in increasing the trafficking of the CF protein out of the ER and its maturation through the Golgi. During its biosynthesis, CFTR is initially synthesized as a nascent polypeptide chain in the rough ER, with a molecular weight of around 120 kDa (Band A). It rapidly receives a core glycosylation in the ER, giving it a molecular weight of around 140 kDa (Band B). As CFTR exits the ER and matures through the Golgi stacks, its glycosylation is modified until it achieves a terminal mature glycosylation, affording it a molecular weight of around 170 kDa (Band C). Thus, the extent to which CFTR exits the ER and traverses the Golgi to reach the plasma membrane may be reflected in the ratio of Band B to Band C protein. CFTR is immunoprecipitated from control cells, and cells exposed to test compounds. Both wt CFTR and ΔF508 CFTR expressing cells are tested. Following lysis, CFTR is immunoprecipitated using various CFTR antibodies. Immunoprecipitates are then subjected to in vitro phosphorylation using radioactive ATP and exogenous protein kinase A. Samples are subsequently solubilized and resolved by SDS-PAGE. Gels are then dried and subject to autoradiography and phosphor image analysis for quantitation of Bands B and C are determined on a BioRad personal fix image station.

Furthermore, compounds of this invention can be used to treat homozygous β thalassemia, a disease in which there is inadequate production of β globin leading to severe anemia. See Collins et al., Blood, 85(1), 43-49 (1995).

Still further, compounds described herein are evaluated for their use as antiprotozoal or antiparasitic agents. The evaluation can be conducted using parasite cultures (e.g., Asexual P. falciparum). See Trager, W. & Jensen, J. B. Science 193, 673-675 (1976). Test compounds are dissolved in dimethyl sulfoxide (DMSO) and added to wells of a flat-bottomed 96-well microtitre plate containing human serum. Parasite cultures are then added to the wells, whereas control wells only contain parasite cultures and no test compound. After at least one invasion cycle, and addition of labeled hypoxanthine monohydrochloride, the level of incorporation of labeled hypoxanthine is detected. IC₅₀ values can be calculated from data using a non-linear regression analysis.

The toxicity of a compound described herein is evaluated when a compound is administered by single intraperitoneal dose to test mice. After administration of a predetermined dose to three groups of test mice and untreated controls, mortality/morbidity checks are made daily. Body weight and gross necropsy findings are also monitored. For reference, see Gad, S. C. (ed.), Safety Assessment for Pharmaceuticals (Van Nostrand Reinhold, N.Y., 1995).

The following specific examples, which described syntheses, screening, and biological testing of various compounds of this invention, are therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. All publications recited herein, including patents, are hereby incorporated by reference in their entirety.

Example 1 Synthesis of 3-methyl-5-phenyl-2,4-pentadienoic acid

To a cooled (−10 to −5° C.) 165 mL of 3 M solution of methyl magnesium iodide in ether was added dropwise a solution of ethyl trans-cinnamate (25.0 g) in 200 mL of anhydrous ether. The reaction was warmed to room temperature and stirred overnight. The mixture was then heated up to 33° C. under reflux for two hours and cooled to 0° C. A white solid was formed during cooling and water (105 mL) was gradually added to dissolve the white precipitate followed by an additional 245 mL of saturated aqueous ammonium chloride solution. The mixture was then stirred until the solids were completely dissolved and extracted with 100 mL of ether three times. The combined extract was washed with 100 mL of water, dried over anhydrous sodium sulfate and filtered. The solvent was evaporated to give 22.1 g of the desired 4-phenyl-2-methyl-3-buten-2-ol as an oil which was used in the next step without further purification. ¹H NMR (CDCl₃, 300 MHz), δ(ppm) 7.41 (m, 5H), 6.58 (d, 1H), 6.34 (d, 1H), 1.41 (broad s, 6H).

Dimethylformamide (DMF, anhydrous, 25 mL) was cooled to 0-5° C. and phosphorus oxychloride (16.4 mL) was added dropwise over a period of an hour. The resulting solution was added dropwise to a cooled (0-5° C.) solution of 4-phenyl-2-methyl-3-buten-2-ol (0.14 mol) in 60 mL of anhydrous DMF over a period of an hour. The reaction mixture was then warmed to room temperature, gradually heated up to 80° C., stirred at 80° C. for three hours and cooled to 0-5° C. To the cooled reaction solution was added dropwise a solution of sodium acetate (80 g) in deionized water (190 mL) over a period of two hours. The mixture was then reheated to 80° C., stirred at 80° C. for an additional 10 minutes, cooled down to room temperature and extracted with ether (300 mL) twice. The combined extract was washed with water (200 mL), dried over anhydrous sodium sulfate, filtered and concentrated in vacuum to yield 16.7 g of the desired 3-methyl-5-phenyl-2,4-pentadienal as a liquid which was used in the next step without further purification.

To a stirred solution of 3-methyl-5-phenyl-2,4-pentadienal (16.5 g) in ethanol (330 mL) was added dropwise a solution of silver nitrate (19.28 g) in water (160 mL) followed by dropwise addition of an aqueous sodium hydroxide (25 g, 80 mL) solution. The resulting mixture was allowed to stir for an additional five hours and then filtered. The solid was washed with ethanol. The combined filtrate was concentrated in vacuum. The residue was dissolved in water (200 mL). The aqueous solution was extracted with ether (300 mL) twice and acidified with 6 N hydrochloric acid (74 mL). The solid formed was filtered and recrystallized from methanol (40 mL) to yield 2.65 g of the desired 3-methyl-5-phenyl-2,4-pentadienoic acid. ¹H NMR (acetone-d₆, 300 MHz), δ(ppm) 7.60 (d, 2H), 7.35 (m, 3H), 7.06 (m, 2H), 6.02 (broad s, 1H), 2.50 (s, 3H).

Example 2 Synthesis of 4-methyl-5-phenyl-2,4-pentadienoic acid

Butyllithium (135 mL of 2.5 N solution) was added to 600 mL of anhydrous tetrahydrofuran (THF) at −65° C. A solution of diethylphosphonoacetic acid (30.5 g) in 220 mL of anhydrous THF was added dropwise to the stirred solution at −65° C. over a period of 60 minutes. The resulting solution was stirred at −65° C. for an additional 30 minutes and then a solution of α-methyl-trans-cinnamaldehyde (23.2 g) in 100 mL of anhydrous THF was added to the reaction at −65° C. over a period of 70 minutes. The reaction was stirred for one hour, allowed to warm to room temperature and then stirred overnight. The reaction was then acidified with 5% hydrochloric acid (125 mL) to a pH of 2.8. The aqueous layer was extracted with 100 mL of ether twice and with 100 mL of ethyl acetate once. The combined organic extract was dried over anhydrous sodium sulfate, filtered and concentrated under vacuum. The crude material was dissolved in 100 mL of hot methanol and then refrigerated overnight. The crystals formed were filtered and dried under vacuum to afford 25.8 g of the desired 4-methyl-5-phenyl-2,4-pentadienoic acid. ¹H NMR (acetone-d₆, 300 MHz), δ(ppm) 7.53 (d, 1H), 7.43 (m, 4H), 7.37 (dd, 1H), 6.97 (broad s, 1H), 6.02 (d, 1H), 2.07 (s, 3H).

Example 3 Synthesis of 4-chloro-5-phenyl-2,4-pentadienoic acid

Butyllithium (50 mL of 2.5 N solution) was added to 250 mL of anhydrous tetrahydrofuran (THF) at −65° C. A solution of diethylphosphonoacetic acid (11.4 g) in 90 mL of anhydrous THF was added dropwise to the stirred solution at −65° C. The resulting solution was stirred at −65° C. for an additional 40 minutes and then a solution of α-chloro-cinnamaldehyde (10.0 g) in 60 mL of anhydrous THF was added to the reaction at −65° C. over a period of 95 minutes. The reaction was stirred for one hour, allowed to warm to room temperature and then stirred overnight. The reaction was then acidified with 5% hydrochloric acid (48 mL) to a pH of 3.9. The aqueous layer was extracted with 50 mL of ether twice and with 50 mL of ethyl acetate once. The combined organic extract was dried over anhydrous sodium sulfate, filtered and concentrated under vacuum. The crude material was dissolved in 30 mL of hot methanol and then refrigerated overnight. The crystals formed were filtered and dried under vacuum to afford 9.2 g of the desired 4-chloro-5-phenyl-2,4-pentadienoic acid. ¹H NMR (acetone-d₆, 300 MHz), δ(ppm) 7.86 (d, 2H), 7.60 (d, 1H), 7.45 (m, 3H), 7.36 (broad s, 1H), 6.32 (d, 1H).

Example 4 Synthesis of 5-phenyl-2-ene-4-pentynoic acid

Butyllithium (16 mL of 2.5 N solution) was added to 75 mL of anhydrous tetrahydrofuran (THF) at −65° C. A solution of diethylphosphonoacetic acid (3.6 g) in 25 mL of anhydrous THF was added dropwise to the stirred solution at −65° C. over a period of 15 minutes. The resulting solution was stirred at −65° C. for an additional 30 minutes and then a solution of phenylpropargyl aldehyde (2.5 g) in 20 mL of anhydrous THF was added to the reaction at −65° C. over a period of 20 minutes. The reaction was stirred for one hour, allowed to warm to room temperature and then stirred overnight. The reaction was then acidified with 6 N hydrochloric acid (5 mL) to a pH of 1.0. The aqueous layer was extracted with 75 mL of ethyl acetate three times. The combined organic extract was dried over anhydrous sodium sulfate, filtered and concentrated under vacuum. The crude material was recrystallized with chloroform:ether (90:10) and then refrigerated overnight. The crystals were filtered and dried under vacuum to afford 1.1 g of the desired 5-phenyl-2-ene-4-pentynoic acid. ¹H NMR (acetone-d₆, 300 MHz), δ(ppm) 7.50 (m, 5H), 6.98 (d, 1H), 6.35 (d, 1H).

Example 5 Synthesis of 5-(p-dimethylaminophenyl)-2,4-pentadienoic acid

Butyllithium (24 mL of 2.5 N solution) was added to 120 mL of anhydrous tetrahydrofuran (THF) at −65° C. A solution of diethylphosphonoacetic acid (5.5 g) in 45 mL of anhydrous THF was added dropwise to the stirred solution at −65° C. over a period of one hour. The resulting solution was stirred at −65° C. for an additional 30 minutes and then a solution of p-dimethylaminocinnamaldehyde (5.0 g) in 80 mL of anhydrous THF was added to the reaction at −65° C. over a period of 30 minutes. The reaction was stirred for one hour, allowed to warm to room temperature and then stirred overnight. The reaction was then quenched with 400 mL of water and extracted with 300 mL of ethyl acetate three times. The aqueous layer was acidified with 5% hydrochloric acid (11 mL) to a pH of 6.1. The solid formed was filtered, washed with 75 mL of water and dried to yield 3.83 g of the desired 5-(p-dimethylaminophenyl)-2,4-pentadienoic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.34 (m, 3H), 6.82 (m, 2H), 6.70 (d, 2H), 5.84 (d, 1H), 2.94 (s, 6H).

Example 6 Synthesis of 5-(2-furyl)-2,4-pentadienoic acid

Butyllithium (70 mL of 2.5 N solution) was added to 350 mL of anhydrous tetrahydrofuran (THF) at −65° C. A solution of diethylphosphonoacetic acid (15.9 g) in 130 mL of anhydrous THF was added dropwise to the stirred solution at −65° C. over a period of 75 minutes. The resulting solution was stirred at −65° C. for an additional 30 minutes and then a solution of trans-3-(2-furyl)acrolein (10.0 g) in 85 mL of anhydrous THF was added to the reaction at −65° C. over a period of 2 hours. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was then acidified with 5% hydrochloric acid (85 mL) to a pH of 3.5 followed by addition of 30 mL of water. The aqueous layer was extracted with 50 mL of ether twice and with 50 mL of ethyl acetate once. The combined organic extract was dried over anhydrous sodium sulfate, filtered and concentrated under vacuum to give an oil. The crude oil was dissolved in 45 mL of hot methanol and then refrigerated overnight. The crystals formed were filtered and dried under vacuum to afford 9.2 g of the desired 5-(2-furyl)-2,4-pentadienoic acid. ¹H NMR (acetone-d₆, 300 MHz), δ(ppm) 7.64 (broad s, 1H), 7.42 (m, 1H), 6.86 (m, 2H), 6.58 (m, 2H), 6.05 (d, 1H).

Example 7 Synthesis of 6-phenyl-3,5-hexadienoic acid

Triphenylphosphine (178.7 g) and 3-chloropropionic acid (73.9 g) were mixed in a 1-liter 3-neck round bottom flask equipped with a mechanical stirrer, reflux condenser with a nitrogen inlet and a thermocouple. The mixture was heated to 145° C. under nitrogen and stirred for 2 hours. The reaction was then cooled to 70° C. Ethanol (550 mL) was added and the mixture was refluxed at 80° C. until complete dissolution. The solution was cooled to room temperature and ether (900 mL) was added. The mixture was placed in the freezer overnight. The solids were collected by filtration and dried under vacuum to afford 217 g of 3-(triphenylphosphonium)propionic acid chloride as a white solid which was used in the next step without further purification.

Sodium hydride (12.97 g) in an oven dried 5-liter 3-neck round bottom flask equipped with a mechanical stirrer and a thermocouple was cooled to 0-5° C. in an ice bath. A solution of 3-(triphenylphosphonium)propionic acid chloride (100.0 g) and trans-cinnamaldehyde (34 mL) in 400 mL each of anhydrous dimethyl sulfoxide and tetrahydrofuran was added over a period of 3 hours. The reaction was then allowed to warm to room temperature and stirred overnight. The reaction mixture was cooled to 0-5° C. in an ice bath and water (1.6 liters) was added dropwise. The aqueous solution was acidified with 12 N hydrochloric acid (135 mL) to a pH of 1 and extracted with ethyl acetate (1.6 liters) twice. The combined organic layers was washed with water (1000 mL) three times, dried over anhydrous sodium sulfate and concentrated under vacuum to afford a yellow oil. The crude oil was dissolved in 125 mL of methylene chloride and chromatographed on a Biotage 75L silica gel column and eluted with methylene chloride:ether (9:1). The fractions containing the desired product were combined and the solvents were removed under vacuum to afford 10.38 g of 6-phenyl-3,5-hexadienoic acid. ¹H NMR (CDCl₃, 300 MHz), δ(ppm) 7.33 (m, 5H), 6.80 (m, 1H), 6.53 (d, 1H), 6.34 (m, 1H), 5.89 (m, 1H), 3.25 (d, 2H).

Example 8 Synthesis of 7-phenyl-2,4,6-heptatrienoic acid

To a cooled (0-55° C.) 927 mL of 1 M solution of phenyl magnesium bromide in tetrahydrofuran was added dropwise a solution of crotonaldehyde (65.0 g) in 130 mL of anhydrous ether over a period of 2 hours and 45 minutes. The reaction was stirred for an additional 45 minutes and then warmed to room temperature. After four more hours of stiffing, saturated ammonium chloride aqueous solution (750 mL) was added to the reaction. The mixture was extracted with 750 mL of ether twice. The combined extract was dried over anhydrous potassium carbonate and filtered. The solvent was evaporated to give 135.88 g (99.9%) of the desired 1-phenyl-2-buten-1-ol as an oil which was used in the next step without further purification.

1-Phenyl-2-buten-1-ol (135.88 g) was dissolved in 2300 mL of dioxane and treated with 2750 mL of dilute hydrochloric acid (2.3 mL of concentrated hydrochloric acid in 2750 mL of water) at room temperature. The mixture was stirred overnight and then poured into 4333 mL of ether and neutralized with 2265 mL of saturated aqueous sodium bicarbonate. The aqueous phase was extracted with 1970 mL of ether. The combined extract was dried over anhydrous potassium carbonate. Evaporation of the solvent followed by Kugelrohr distillation at 30° C. for 30 minutes afforded 131.73 g (96.8%) of the desired 4-phenyl-3-buten-2-ol as an oil which was used in the next step without further purification.

Dimethylformamide (DMF, anhydrous, 14 mL) was cooled to 0-5° C. and phosphorus oxychloride (8.2 mL) was added dropwise over a period of 40 minutes. The resulting solution was added dropwise to a cooled (0-5° C.) solution of 4-phenyl-3-buten-2-ol (10 g) in 32 mL of anhydrous DMF over a period of an hour. The reaction mixture was warmed to room temperature over a 35-minute period and then gradually heated up to 80° C. over a period of 45 minutes. The reaction was stirred at 80° C. for three hours and then cooled to 0-5° C. To the cooled reaction solution was added dropwise a solution of sodium acetate (40 g) in deionized water (100 mL) over a period of one hour. The mixture was then reheated to 80° C., stirred at 80° C. for an additional 10 minutes, cooled down to room temperature and extracted with ether (100 mL) twice. The combined extract was washed with brine (100 mL), dried over anhydrous sodium sulfate, filtered and concentrated under vacuum to yield 8.78 g of the desired 5-phenyl-2,4-pentadienal as a liquid which was used in the next step without further purification. ¹H NMR (CDCl₃, 300 MHz), δ(ppm) 7.51 (m, 2H), 7.37 (m, 3H), 7.26 (m, 1H), 7.01 (m, 2H), 6.26 (m, 1H).

Butyllithium (12.8 mL of 2.5 N solution) was added to 65 mL of anhydrous tetrahydrofuran (THF) at −65° C. A solution of diethylphosphonoacetic acid (2.92 g) in 25 mL of anhydrous THF was added dropwise to the stirred solution at −65° C. The resulting solution was stirred at −65° C. for an additional 30 minutes and then a solution of 5-phenyl-2,4-pentadienal (2.4 g) in 15 mL of anhydrous THF was added to the reaction at −65° C. The reaction was stirred for one hour, allowed to warm to room temperature and then stirred overnight. To the reaction was added 30 mL of water, acidified with 5% hydrochloric acid (14 mL) to a pH of 4.7 and then added an additional 20 mL of water. The aqueous layer was extracted with 10 mL of ether twice and with 10 mL of ethyl acetate once. The combined organic extract was dried over anhydrous sodium sulfate, filtered and concentrated under vacuum. The crude material was dissolved in 50 mL of hot methanol and then refrigerated overnight. The crystals formed were filtered and dried under vacuum to afford 2.4 g of the desired 7-phenyl-2,4,6-heptatrienoic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.52 (m, 2H), 7.33 (m, 4H), 7.06 (m, 1H), 6.86 (m, 2H), 6.58 (m, 1H), 5.95 (d, 1H).

Example 9 Synthesis of 8-phenyl-3,5,7-octatrienoic acid

A solution of 5-phenyl-2,4-pentadienal (15 g) and 3-(triphenylphosphonium)-propionic acid chloride (35.2 g) in 140 mL each of anhydrous tetrahydrofuran and anhydrous dimethyl sulfoxide was added dropwise to sodium hydride (4.6 g) at 0-5° C. under nitrogen over a period of four hours. The reaction was allowed to warm to room temperature and stirred overnight. The reaction mixture was cooled to 0-5° C. and water (280 mL) was added dropwise over a period of 30 minutes. The aqueous layer was extracted with ethyl acetate (280 mL) twice, acidified with 12 N hydrochloric acid (24 mL) to a pH of 1, extracted again with ethyl acetate (280 mL) twice. The combined organic layers were washed with water (500 mL) twice, dried over anhydrous sodium sulfate and concentrated under vacuum to give an oil. The oily crude product was chromatographed on a Biotage 40M silica gel column and eluted with methylene chloride:ethyl acetate (95:5). The fractions containing the desired product were combined and the solvents were removed under vacuum to afford 0.7 g of 8-phenyl-3,5,7-octatrienoic acid. ¹H NMR (acetone-d₆, 300 MHz), δ(ppm) 7.46 (m, 2H), 7.26 (m, 3H), 6.95 (m, 1H), 6.60 (d, 1H), 6.34 (m, 3H), 5.87 (m, 1H), 3.17 (d, 2H).

Example 10 Synthesis of potassium 2-oxo-6-phenyl-3,5-hexadienoate

A solution of trans-cinnamaldehyde (26.43 g) and pyruvic acid (11.9 mL) in 10 mL of methanol was stirred and chilled to 0-5° C. in an ice bath. To the chilled solution was added 35 mL of potassium hydroxide (16.83 g in 50 mL of methanol) over a period of 20 minutes. The remaining methanolic potassium hydroxide was added rapidly and the ice bath was removed. The solution changed from a yellow to a dark orange and the precipitate was formed. The reaction mixture was chilled in the refrigerator overnight and the solid was collected by filtration, washed with 50 mL of methanol three times, 50 mL of ether and then air dried to afford 29.3 g of the desired 2-oxo-6-phenyl-3,5-hexadienoate as a yellow solid (61.0%). ¹H NMR (DMSO-d₆/D₂O, 300 MHz), δ(ppm) 7.48 (d, 2H), 7.28 (m, 4H), 7.12 (d, 2H), 6.27 (d, 1H).

Example 11 Synthesis of potassium 2-oxo-8-phenyl-3,5,7-octatrienoate

To a cooled (0-55° C.) 927 mL of 1 M solution of phenyl magnesium bromide in tetrahydrofuran was added dropwise a solution of crotonaldehyde (65.0 g) in 130 mL of anhydrous ether over a period of 2 hours and 45 minutes. The reaction was stirred for an additional 45 minutes and then warmed to room temperature. After four more hours of stirring, saturated ammonium chloride aqueous solution (750 mL) was added to the reaction. The mixture was extracted with 750 mL of ether twice. The combined extract was dried over anhydrous potassium carbonate and filtered. The solvent was evaporated to give 135.88 g (99.9%) of the desired 1-phenyl-2-buten-1-ol as an oil which was used in the next step without further purification.

1-Phenyl-2-buten-1-ol (135.88 g) was dissolved in 2300 mL of dioxane and treated with 2750 mL of dilute hydrochloric acid (2.3 mL of concentrated hydrochloric acid in 2750 mL of water) at room temperature. The mixture was stirred overnight and then poured into 4333 mL of ether and neutralized with 2265 mL of saturated sodium bicarbonate. The aqueous phase was extracted with 1970 mL of ether. The combined extract was dried over anhydrous potassium carbonate. Evaporation of the solvent followed by Kugelrohr distillation at 30° C. for 30 minutes afforded 131.73 g (96.8%) of the desired 4-phenyl-3-buten-2-ol as an oil which was used in the next step without further purification.

Dimethylformamide (DMF, anhydrous, 14 mL) was cooled to 0-5° C. and phosphorus oxychloride (8.2 mL) was added dropwise over a period of 40 minutes. The resulting solution was added dropwise to a cooled (0-5° C.) solution of 4-phenyl-3-buten-2-ol (10 g) in 32 mL of anhydrous DMF over a period of an hour. The reaction mixture was warmed to room temperature over a 35-minute period and then gradually heated up to 80° C. over a period of 45 minutes. The reaction was stirred at 80° C. for three hours and then cooled to 0-5° C. To the cooled reaction solution was added dropwise a solution of sodium acetate (40 g) in deionized water (100 mL) over a period of one hour. The mixture was then reheated to 80° C., stirred at 80° C. for an additional 10 minutes, cooled down to room temperature and extracted with ether (100 mL) twice. The combined extract was washed with brine (100 mL), dried over anhydrous sodium sulfate, filtered and concentrated under vacuum to yield 8.78 g of the desired 5-phenyl-2,4-pentadienal as a liquid which was used in the next step without further purification. ¹H NMR (CDCl₃, 300 MHz), δ(ppm) 7.51 (m, 2H), 7.37 (m, 3H), 7.26 (m, 1H), 7.01 (m, 2H), 6.26 (m, 1H).

A solution of 5-phenyl-2,4-pentadienal (6.70 g) and pyruvic acid (3.0 mL) in 5 mL of methanol was stirred and chilled to 0-5° C. in an ice bath. To the chilled solution was added a solution of 35 mL of potassium hydroxide (3.5 g) in 10 mL of methanol dropwise over a period of 30 minutes. The remaining methanolic potassium hydroxide was added rapidly and the ice bath was removed. The reaction was allowed to warm to room temperature and stirred for another hour. The flask was then refrigerated overnight. The solid was collected by filtration, washed with 15 mL of methanol three times, 15 mL of ether and then air dried to afford 6.69 g of potassium 2-oxo-8-phenyl-3,5,7-octatrienoate as a yellow solid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.52 (d, 2H), 7.32 (m, 3H), 7.10 (m, 2H), 6.83 (dd, 2H), 6.57 (dd, 1H), 6.13 (d, 1H).

Example 12 Synthesis of Cinnamoylhydroxamic Acid

Triethylamine (TEA, 17.6 mL) was added to a cooled (0-5° C.) solution of trans-cinnamic acid (15.0 g) in 200 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (16.4 mL). The reaction mixture was stirred for 30 minutes and hydroxylamine hydrochloride (17.6 g) was added followed by dropwise addition of 35 mL of TEA at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was quenched with 250 mL of 1% (by weight) citric acid solution and 50 mL of 5% (by weight) citric acid solution and then extracted with 200 mL of methylene chloride twice and 200 mL of ether once. The solvents were removed under vacuum. The residue was triturated with 125 mL of water, filtered, washed with 25 mL of water and dried under vacuum to give a tan solid. The crude product was chromatographed on a Biotage 75S column and eluted with methylene chloride:acetonitrile (80:20). The fractions containing the desired product were combined and the solvent was removed under vacuum to yield 4.1 g of cinnamoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.48 (m, 6H), 6.49 (d, 1H).

Example 13 Synthesis of N-methyl-cinnamoylhydroxamic acid

A solution of cinnamoyl chloride (5 g) in 50 mL of methylene chloride was added dropwise to a solution of N-methylhydroxylamine hydrochloride (5 g) and 12 mL of 40% sodium hydroxide in 50 mL of water cooled to 0-5° C. The reaction mixture was stirred for two hours. The aqueous layer was acidified with concentrated hydrochloric acid. The precipitate was collected by filtration and dried under vacuum to afford 2.8 g of the desired N-methyl-cinnamoylhydroxamic acid as a white solid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.66 (d, 2H), 7.53 (d, 1H), 7.42 (m, 3H), 7.26 (d, 1H), 3.22 (s, 3H).

Example 14 Synthesis of 5-phenyl-2,4-pentadienoylhydroxamic acid

Triethylamine (TEA, 29 mL) was added to a cooled (0-5° C.) solution of 5-phenyl-2,4-pentadienoic acid (29.0 g) in 300 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (27.0 mL). The reaction mixture was stirred for 15 minutes and hydroxylamine hydrochloride (28.92 g) was added followed by dropwise addition of 58 mL of TEA over a period of 60 minutes at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was then poured into 450 mL of a 1% (by weight) solution of citric acid and then extracted with 200 mL of methylene chloride twice and 500 mL of ether once. The solvents were removed under vacuum to give an oil. The crude oil was crystallized with 200 mL of hot acetonitrile to give a tan solid. The tan solid was recrystallized from 60 mL of hot acetonitrile to afford 12.5 g of the desired 5-phenyl-2,4-pentadienoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.56 (d, 2H), 7.31 (m, 4H), 7.03 (m, 2H), 6.05 (s, 1H).

Example 15 Synthesis of N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid

5-Phenyl-2,4-pentadienoic acid (6 g) and oxalyl chloride (6.1 mL) were dissolved in 50 mL of methylene chloride and 0.2 mL of dimethylformamide was added. The reaction was stirred for three hours, concentrated under vacuum and then co-evaporated with 100 mL of chloroform to remove oxalyl chloride. The crude 5-phenyl-2,4-pentadienoic acid chloride was used in the next step without further purification.

5-Phenyl-2,4-pentadienoic acid chloride was dissolved in 50 mL of methylene chloride and added to a solution of 13.8 mL of 40% sodium hydroxide in 50 mL of water at 0-5° C. The resulting solution was stirred for two hours and then acidified to a pH of 4 with concentrated hydrochloric acid. The precipitate was collected by filtration and dried under vacuum to afford 4.2 g of N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.57 (d, 2H), 7.35 (m, 4H), 7.19 (m, 1H), 6.99 (d, 1H), 6.82 (d, 1H), 3.21 (s, 3H).

Example 16 Synthesis of 3-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid

Triethylamine (TEA, 1.8 mL) was added to a cooled (0-5° C.) solution of 3-methyl-5-phenyl-2,4-pentadienoic acid (2.0 g) in 20 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (1.7 mL) over a period of 15 minutes. The reaction mixture was stirred for 30 minutes and hydroxylamine hydrochloride (1.85 g) was added followed by dropwise addition of 3.7 mL of TEA over a period of 35 minutes at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. To the stirred reaction mixture at room temperature was added 20 mL of a 1% (by weight) solution of citric acid followed by 75 mL of water. The mixture was stirred for 30 minutes and then filtered. The filtered cake was washed with 30 mL of water and dried in vacuum to afford 1.49 g of the desired 3-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid in 69% yield. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.55 (d, 2H), 7.30 (m, 3H), 6.89 (broad s, 2H), 5.83 (s, 1H), 2.38 (s, 3H).

Example 17 Synthesis of 4-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid

Triethylamine (TEA, 6.5 mL) was added to a cooled (0-5° C.) solution of 4-methyl-5-phenyl-2,4-pentadienoic acid (7.0 g) in 75 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (6.0 mL) over a period of 60 minutes. The reaction mixture was stirred for 15 minutes and hydroxylamine hydrochloride (6.5 g) was added followed by dropwise addition of 13 mL of TEA over a period of 60 minutes at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. To the stirred reaction mixture at room temperature was added 130 mL of a 1% (by weight) solution of citric acid followed by 50 mL of water. The mixture was stirred for 30 minutes and then filtered. The filtered cake was recrystallized from hot acetonitrile to afford 4.4 g of the desired 4-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.37 (m, 6H), 6.91 (s, 1H), 6.02 (d, 1H), 1.99 (s, 3H).

Example 18 Synthesis of 4-chloro-5-phenyl-2,4-pentadienoylhydroxamic acid

Triethylamine (TEA, 2.5 mL) was added to a cooled (0-5° C.) solution of 4-chloro-5-phenyl-2,4-pentadienoic acid (3.0 g) in 30 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (2.3 mL) over a period of 15 minutes. The reaction mixture was stirred for 30 minutes and hydroxylamine hydrochloride (2.5 g) was added followed by dropwise addition of 5.0 mL of TEA over a period of 60 minutes at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was then quenched with 30 mL of a 1% (by weight) solution of citric acid followed by 115 mL of water. The mixture was stirred for 30 minutes and then filtered. The filtered cake was washed with 100 mL of water and dried under vacuum. The crude material was recrystallized from 20 mL of hot acetonitrile twice to yield 1.46 g of the desired 4-chloro-5-s phenyl-2,4-pentadienoylhydroxamic acid as a solid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.75 (d, 2H), 7.40 (m, 5H), 6.31 (d, 1H).

Example 19 Synthesis of 5-phenyl-2-ene-4-pentynoylhydroxamic acid

Triethylamine (TEA, 1.1 mL) was added to a cooled (0-5° C.) solution of 5-phenyl-2-ene-4-pentynoic acid (1.1 g) in 13 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (1.0 mL). The reaction mixture was stirred for 30 minutes and hydroxylamine hydrochloride (1.1 g) was added followed by dropwise addition of 2.2 mL of TEA at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was quenched with 15 mL of a 1% (by weight) solution of citric acid and extracted with 30 mL of methylene chloride twice. The combined organic layer was dried over anhydrous sodium sulfate. The solvents were removed under vacuum to give an oil which in turn was triturated with 10 mL of chloroform. The solid was collected by filtration to yield 0.63 g of the desired 5-phenyl-2-ene-4-pentynoylhydroxamic acid as a white powder. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.48 (m, 5H), 6.76 (d, 1H), 6.35 (d, 1H).

Example 20 Synthesis of 5-(p-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid

Triethylamine (TEA, 0.8 mL) was added to a cooled (0-5° C.) solution of 5-(p-dimethylaminophenyl)-2,4-pentadienoic acid (1.0 g) in 10 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (0.7 mL). The reaction mixture was stirred for 60 minutes and hydroxylamine hydrochloride (0.8 g) was added followed by dropwise addition of 1.6 mL of TEA at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was quenched with 15 mL of water. The solid was filtered and dried under vacuum to yield 0.75 g of the desired 5-(p-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.33 (m, 3H), 6.86 (m, 2H), 6.70 (d, 2H), 5.84 (d, 1H), 2.99 (s, 6H).

Example 21 Synthesis of 5-(2-furyl)-2,4-pentadienoylhydroxamic acid

Triethylamine (TEA, 2.1 mL) was added to a cooled (0-5° C.) solution of 5-(2-furyl)-2,4-pentadienoic acid (2.0 g) in 15 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (2.0 mL) over a period of 30 minutes. The reaction mixture was stirred for 30 minutes and hydroxylamine hydrochloride (2.15 g) was added followed by dropwise addition of 4.2 mL of TEA over a period of 60 minutes at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. To the stirred reaction mixture at room temperature was added 12 mL of a 1% (by weight) solution of citric acid followed by 46 mL of water. The mixture was stirred for 30 minutes and then filtered. The filtered cake was washed with 30 mL of water and dried in vacuum to afford 1.3 g of the desired 5-(2-furyl)-2,4-pentadienoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.73 (broad s, 1H), 7.22 (m, 1H), 6.71 (m, 4H), 6.01 (d, 1H).

Example 22 Synthesis of 6-phenyl-3,5-hexadienoylhydroxamic acid

Triethylamine (TEA, 1.75 mL) was added to a cooled (0-5° C.) solution of 6-phenyl-3,5-hexadienoic acid (2.0 g) in 30 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (1.62 mL) over a period of 15 minutes. The reaction mixture was stirred for 15 minutes and hydroxylamine hydrochloride (1.74 g) was added followed by dropwise addition of 3.5 mL of TEA at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. The reaction was then poured into 20 mL of 1% (by weight) aqueous citric acid solution and extracted with 20 mL of methylene chloride twice and ether once. The combined organic layer was dried over anhydrous sodium sulfate and concentrated under vacuum to give a dark red oil. The crude oil was crystallized with 10 mL of hot acetonitrile. The solid was collected by filtration and then purified on a Biotage 40S silica gel column using methylene chloride:ether (95:5) as an eluent. The fractions containing the desired product were combined and the solvent was removed to give 40 mg of 6-phenyl-3,5-hexadienoylhydroxamic acid as a tan solid (2.1%). ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.34 (m, 5H), 6.91 (m, 1H), 6.55 (d, 1H), 6.30 (m, 1H), 5.89 (m, 1H), 3.36 (d, 2H).

Example 23 Synthesis of N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid

6-Phenyl-3,5-hexadienoic acid (1 g) was dissolved in 10 mL of tetrahydrofuran (THF) and treated with 0.9 g of 1,1′-carbonyldiimidazole. The reaction was stirred for 30 minutes. N-methylhydroxylamine hydrochloride (0.44 g) was neutralized with 0.29 g of sodium methoxide in 10 mL of THF and 5 mL of methanol and then filtered to remove the sodium chloride. N-methylhydroxylamine was then added to the reaction mixture and stirred overnight. The resulting mixture was partitioned between 25 mL of water and 50 mL of ethyl acetate. The ethyl acetate layer was washed with 25 mL each of 5% hydrochloric acid, saturated sodium bicarbonate and brine, dried over sodium sulfate and concentrated under vacuum to afford 0.9 g of a viscous yellow oil. The crude product was chromatographed on a Biotage 40S silica gel column and eluted with ethyl acetate:hexane (1:1). The fractions containing the desired product were combined and the solvent was removed under vacuum to yield 0.17 g of N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid. ¹H NMR (CDCl₃, 300 MHz), δ(ppm) 7.38 (m, 5H), 6.80 (m, 1H), 6.60 (m, 1H), 6.35 (m, 1H), 5.89 (m, 1H), 3.24 (m, 2H), 2.92 (s, 3H).

Example 24 Synthesis of 7-phenyl-2,4,6-heptatrienoylhydroxamic acid

Triethylamine (TEA, 24.1 mL) was added to a cooled (0-5° C.) solution of 7-phenyl-2,4,6-heptatrienoic acid (27.8 g) in 280 mL of anhydrous dimethylformamide. To this solution was added dropwise isobutyl chloroformate (22.5 mL) over a period of 75 minutes. The reaction mixture was stirred for 40 minutes and hydroxylamine hydrochloride (24.2 g) was added followed by dropwise addition of 48 mL of TEA over a period of 70 minutes at 0-5° C. The reaction was allowed to warm to room temperature and stirred overnight. To the stirred reaction mixture at room temperature was added 280 mL of a 1% (by weight) solution of citric acid followed by 1050 mL of water. The mixture was stirred for 30 minutes and then filtered. The filtered cake was washed with water (200 mL) and dried under vacuum to afford 20.5 g of the desired 7-phenyl-2,4,6-heptatrienoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.48 (m, 2H), 7.32 (m, 2H), 7.19 (m, 2H), 7.01 (m, 1H), 6.75 (m, 2H), 6.51 (m, 1H), 5.93 (d, 1H).

Example 25 Synthesis of 4-cyclohexylbutyroylhydroxamic acid

To a solution of hydroxylamine hydrochloride (7.3 g) in 50 mL of methanol was added 24 mL of sodium methoxide (25% wt.) dropwise at room temperature over a period of 45 minutes. To this solution was added methyl 4-cyclohexylbutyrate in 50 mL of methanol at room temperature followed by 12 mL of sodium methoxide (25% wt.) dropwise over a period of 60 minutes. The resulting mixture was stirred at room temperature overnight. The reaction was then poured into 120 mL of water and acidified to a pH of 4 with 45 mL of glacial acetic acid. Methanol was removed under vacuum. The solid formed was filtered and dried over phosphorus pentoxide to afford 8.53 g of the desired 4-cyclohexylbutyroyl-hydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 3.38 (m, 2H), 1.91 (t, 2H), 1.68 (m, 4H), 1.50 (m, 2H), 1.16 (m, 5H), 0.84 (m, 2H).

Example 26 Synthesis of S-benzylthioglycoloylhydroxamic acid

S-benzylthioglycolic acid (12.0 g) was dissolved in 250 mL of methanol and sparged with hydrogen chloride gas at room temperature for 20 minutes. The solvent was then removed under vacuum. Methyl S-benzylthioglycolate obtained was used in the next step without further purification.

To a solution of hydroxylamine hydrochloride (9.2 g) in 60 mL of methanol was added 30 mL of sodium methoxide (25% wt.) dropwise at room temperature over a period of 30 minutes. To this solution was added methyl S-benzylthioglycolate in 50 mL of methanol at room temperature followed by 15 mL of sodium methoxide (25% wt.) dropwise over a period of 60 minutes. The resulting mixture was stirred at room temperature overnight. The reaction was then poured into 150 mL of water and acidified to a pH of 4 with 55 mL of glacial acetic acid. Methanol was removed under vacuum. The solid formed was filtered and dried over phosphorus pentoxide to afford 8.57 g of the desired S-benzylthioglycoloyl-hydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.29 (m, 5H), 3.84 (s, 2H), 2.93 (s, 2H).

Example 27 Synthesis of 5-phenylpentanoloylhydroxamic acid

5-Phenylpentanoic acid (10.0 g) was dissolved in 250 mL of methanol and sparged with hydrogen chloride gas at room temperature for 15 minutes. The solvent was then removed under vacuum. Methyl 5-phenylpentanoate obtained was used in the next step without further purification.

To a solution of hydroxylamine hydrochloride (7.8 g) in 50 mL of methanol was added 26 mL of sodium methoxide (25% wt.) dropwise at room temperature over a period of 45 minutes. To this solution was added methyl 5-phenylpentanoate in 50 mL of methanol at room temperature followed by 15 mL of sodium methoxide (25% wt.) dropwise over a period of 60 minutes. The resulting mixture was stirred at room temperature overnight. The reaction was then poured into 150 mL of water and acidified to a pH of 4 with 40 mL of glacial acetic acid. The solvents were removed under vacuum to give a yellow oil. The yellow oil was placed on a Biotage 40M silica gel column and eluted with methylene chloride:ethanol (95:5). The fractions containing the desired product as indicated by the NMR were combined. The solvents were removed under vacuum to afford 8.30 g of the desired 5-phenylpentanoylhydroxamic acid. ¹H NMR (DMSO-d₆, 300 MHz), δ(ppm) 7.22 (m, 5H), 3.42 (s, 3H), 2.55 (t, 2H), 1.98 (t, 2H), 1.52 (m, 4H).

Example 28 In Vitro Efficacy Studies—Extreme Drug Resistance (EDR) Assay

The PC3 cell line was maintained in RPMI supplemented with 10% fetal calf serum and antibiotics. Cells were suspended in 0.12% soft agar in complete medium and plated (2,000 cells per well) in different drug concentrations onto a 0.4% agarose underlayer in 24-well plates. Plating calls on agarose underlayers supports the proliferation only of the transformed cells, ensuring that the growth signal stems from the malignant component of the tumor.

All compounds were dissolved were dissolved in DMSO to 200× stock solutions. Stock solutions were diluted to 20× working solutions using the tissue culture medium, serially diluted and added to the 24-well plates. The initial range of concentrations was 1 micromolar to 200 micromolar. This concentration range was extended in the case of N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid to 10 μM-500 μM and in the case of tricostatin A to 0.001 μM to 0.3 μM. No significant changes in pH of the culture medium were observed under the above conditions. Diluent control wells contained PC3 cells treated with DMSO, at the dilutions used for appropriate drug treatment. All experimental points were represented by two separate wells (duplicates). Four wells containing tumor cells that were not treated with drugs served as negative controls in each experiment.

Cells were incubated with drugs under standard culture conditions for 5 days. Cultures were pulsed with tritiated thymidine (³H-TdR, New Life Science Products, Boston, Mass.) at 5 μCi per well for the last 48 hours of the culture period. Cell culture plates were then heated to 90° C. to liquefy the agarose, and cells were harvested onto glass fiber filters, which were then placed into counting vials containing liquid scintillation fluid. The radioactivity trapped on the filters was counted with a Beckman scintillation counter. The fraction of surviving cells was determined by comparing ³H-TdR incorporation in treated (experimental points) and untreated (negative control) wells. Microsoft Excel was used to organize the raw data on EDR experiments, and the SigmaPlot program was utilized to generate drug response curves. All drug response curves were as approximated as sigmoidal equations (characteristic for typical drug response curves) to fit the data. IC₅₀ values were determined using the approximated sigmoidal curves and expressed as mM.

IC₅₀ values of the test compounds range from approximately 1 μM to approximately 2000 μM.

Example 29 Histone (Hyper)Acetylation Assay

The model used in this assay was mouse erythroleukemia cells. Specifically, the level of acetylation of H4 histones in these erythroleukemia cells was monitored. H4 histones was chosen as the target due to the ease of resolution of the variably acetylated histones. Inhibition of histone deacetylase leads to increased (hyper)acetylation of histones. Activities on histone deacetylase were examined to confirm the results of this assay. See Example 30 below.

Studies were performed with the DS19 mouse erythroleukemia cells maintained in RPMI 1640 medium with 25 mM HEPES buffer and 5% fetal calf serum. The cells were incubated at 37° C. In studies on proliferation, cell density was determined at 24 hour intervals using a hemacytometer.

Histone Isolation

Histones were isolated from cells after incubation for 2 or 24 hours. The cells were centrifuged for 5 minutes at 2,000 rpm in the Sorvall SS34 rotor and washed once with phosphate buffered saline. The pellets were suspended in 5 mL lysis buffer (10 mM Tris, 50 mM sodium bisulfite, 1% Triton X-100, 10 mM magnesium chloride, 8.6% sucrose, pH 6.5) and homogenized with six strokes of a teflon pestle. The homogenizing tubes were rinsed with 5 mL lysis buffer. The combined solutions were centrifuged and the pellets were washed once with 5 mL of the lysis buffer and once with 5 mL 10 mM Tris, 13 mM EDTA, pH 7.4. The pellets were extracted with 2×1 mL 0.25N HCl. Histones were precipitated from the combined extracts by the addition of 20 mL acetone and refrigeration overnight. The histones were pelleted by centrifuging at 5,000 rpm for 20 minutes in the Sorvall SS34 rotor. The pellets were washed once with 5 mL acetone and protein concentration was quantitated by the Bradford procedure.

Polyacrylamide Gel Electrophoresis

Separation of acetylated histones was performed with an acetic acid-urea polyacrylamide gel electrophoresis procedure as originally described by Panyim and Chalkley Arch. Biochem. Biophys. 130, 337-346, 1969. 25 μg histones were applied to a slab gel which was run at 20 ma. The run was continued for a further two hours after the Pyronin Y tracking dye had run off the gel. The gel was stained with Coomassie Blue R. The most rapidly migrating protein band is the unacetylated H4 histone followed by bands with 1,2,3 and 4 acetyl groups which were quantitated by densitometry.

Densitometry

Densitometry was measured through digital recording using the Alpha Imager 2000. Enlargement of the image was done using PHOTOSHOP (Adobe Corp.) on a MACINTOSH (Apple Corp.) computer. After creating a hard copy of the gel by using a laser printer, a Shimadzu CS9000U densitometer was used to measure densitometry by reflectance. The percentage of H4 histone in the various acetylated states was expressed as a percentage of the total H4 histone.

Results

Many of the test compounds showed EC₅₀ values in micromolar concentration range.

Example 30 Histone Deacetylation Assay

The determination of the inhibition of histone deacetylase by compounds was based upon the procedure described by Hoffmann et al., Nucleic Acids Res. 27, 2057-2058 (1999). The histone deacetylase was isolated from rat liver as previously described in Kolle, D. et al., Methods: A Companion to Methods in Enzymology 15, 323-331 (1998). Compounds were initially dissolved in either ethanol or in DMSO to provide a working stock solution. The synthetic substrate used in the assay is N-(4-methyl-7-coumarinyl)-N-α(tert-butyloxy-carbonyl)-N-Ω-acetyllysineamide (MAL).

The assay was performed in a final total volume of 120 μL consisting of 100 μL of 15 mM tris-HCl buffer at pH 7.9 and 0.25 mM EDTA, 10 mM NaCl, 10% glycerol, 10 mM mercaptoethanol and the enzyme. The assay was initiated upon the addition of 10 μl of a test compound followed by the addition of a fluorescent-labeled lysine substrate to each assay tube in an ice bath for 15 minutes. The tubes were transferred to a water bath at 37° C. for an additional 90 minutes.

An initial assay was performed to determine the range of activity of each test compound. The determination of IC₅₀ values was made from the results of five dilutions in range according to the expected potency for each test compound. Each assay was duplicated or triplicated.

Test compounds showed potent inhibition of histone deacetylase, having IC₅₀ values in the low micromolar concentration range (e.g., two test compounds showed IC₅₀ values of 1.7 μM and 1.8 μM).

Example 31 X-ALD Screening Assay Cell Cultures and Drug Treatment

Cell lines derived from X-ALD human patients were grown in RPMI supplemented with fetal calf serum (10%), penicillin (100 U/mL), streptomycin (100 U/mL) and glutamine (2 mM). On day 0, cells were divided into two separate tissue culture flasks, and test compounds (2.5-250 μM final concentration, diluted from a 0.5 M stock solution in PBS, pH 7.6) was added to one flask. Cells in the second flask were grown in the absence of test compounds for the same length of time and served as controls. The media were changed every 3-4 days.

Biochemical Measurements

As described above, tissue culture cells were grown in the presence or absence of test compounds, collected from tissue culture flasks using trypsin, washed twice with PBS and subjected to biochemical analysis. VLCFA measurements was conducted by extracting total amount of lipids, converted the lipids to methyl ester, purified by TLC, and subjected to capillary CC analysis as described in Moser et al., Technique in Diagnostic Biochemical Genetics: A Laboratory Manual (ed. A., H.F.) 177-191 (Wiley-Liss, New York, 1991). Duplicate assays were set up independently and were assayed on different days. C24:0 β-oxidation activity of lymphoblastoid cells was determined by measuring their capacity to degrade [1-¹⁴C]—C24:0 fatty acid to water-soluble products as described in Watkins et al., Arch. Biochem. Biophys. 289, 329-336 (1991). The statistical significance of measured biochemical differences between untreated and treated X-ALD cells can be determined by a two-tailed Student's t-test.

Compounds were found to decrease the cellular content of the VLCFA by approximately 60 percent in the X-ALD cells.

Example 32 Cystic Fibrosis Screening Assay

As described above, during its biosynthesis, CFTR is initially synthesized as a nascent polypeptide chain in the rough ER, with a molecular weight of around 120 kDa (Band A). It rapidly receives a core glycosylation in the ER, giving it a molecular weight of around 140 kDa (Band B). As CFTR exits the ER and matures through the Golgi stacks, its glycosylation is modified until it achieves a terminal mature glycosylation, affording it a molecular weight of around 170 kDa (Band C). The extent to which CFTR exits the ER and traverses the Golgi to reach the plasma membrane may be reflected in the ratio of Band B to Band C protein. CFTR is immunoprecipitated from control cells, and cells exposed to test compounds. Both wt CFTR and ΔF508 CFTR expressing cells are tested. Following lysis, CFTR are immunoprecipitated using various CFTR antibodies. Immunoprecipitates are then subjected to in vitro phosphorylation using radioactive ATP and exogenous protein kinase A. Samples are subsequently solubilized and resolved by SDS-PAGE. Gels are then dried and subject to autoradiography and phosphor image analysis for quantitation of Bands B and C are determined on a BioRad personal fix image station.

Cell Culture

Chinese hamster ovary (CHO) cells stably expressing both wt and ΔF508 CFTR were used in these assays. The cultures were grown on 100 mm plastic cell dishes in DMEM containing 10% fetal bovine serum (FBS) and kept at 5% CO₂/95% O₂ at 37° C. Cells were grown to confluence and used 3-5 days post-plating. All test compounds were added to cells for 24 hours prior to analysis.

Immunoprecipitation

Cells were treated with test compounds and CFTR immunoprecipitated as described in Bradbury et al., Am. J. Physiol. 276, L659-668 (1999). Briefly, treated cells were lysed in buffer containing 1% TRITON X-100 and various protease inhibitors. Soluble material was immunoprecipitated using both R domain and C-terminal monoclonal antibodies.

Immunoprecipitated CFTR was then subject to in vitro phosphorylation using camp-dependent PKA catalytic subunit and [γ-32P]ATP, followed by resolution on SDS-PAGE gels. After fixation, the gels were dried and processed for autoradiography and phosphor image analysis. Quantitation of B and C bands on a BioRad personal fix image analysis station.

It was found that compounds (at 100 μM) showed no significant changes in the levels of Bands B and C in treated cells relative to untreated cells. Based on the results obtained from using these test compounds, there was no gross effect of the test compounds on the expression levels of wild type CFTR. Analysis of band C of ΔF508 CFTR CHO cells showed that very little Band C was present in ΔF508 cells compared to wild-type cells. Exposure of these cells to test compounds at 100 μM for 24 hours at 37° C. did not affect the level of Band C CFTR in either wild-type or ΔF508 CFTR expressing cells. In contrast, analysis of Band B CFTR in ΔF508 cells showed that test compounds at 100 μM resulted in a significant increase (about 6-7 fold) in the level of Band B compared to ΔF508 cells not exposed to the test compounds.

Example 33 Toxicity Assay

Test compounds were administered to three groups of 10 mice at 100, 300, and 1,000 mg/kg. An additional group received vehicle (20% hydroxypropyl-(3-cyclodextrin aqueous solution) at 10 mL/kg. Mortality/morbidity checks were made twice daily. Clinical observations were recorded predose and/or postdose on Day 1, and daily thereafter through Day 8. Body weights were recorded on the day of dosing (Day 1) and on Day 8. Mice were euthanized by CO₂ asphyxiation and necropsied on Day 8 or upon death.

One test compound was tested so far and based on the results obtained, the no-observed toxicity level for this compound when administered to CD-1 mice as a single intraperitoneal does 100 mg/kg. Clinical signs of toxicity were noted after dosing at 300 mg/kg with recovery within 24 hours, while dosing at 1,000 mg/kg resulted in death (80% of animals) by the end of Day 2.

Example 34 Synthesis of 1-hydroxy-4-phenyl-2-butanone

A solution of 12.33 mL of diisopropylamine in 100 mL of THF was cooled to −25° C. and treated with 8.8 mL of 10M n-butyllithium. After 10 minutes, 12 mL of benzylacetone in 100 mL of THF was added. After 10 minutes, 18.3 mL of chlorotrimethylsilane was added quickly. The resulting mixture was warmed to room temperature and stirred for 2.5 hours. The solution was diluted with pentane (200 mL), washed with cold saturated sodium bicarbonate, dried over sodium sulfate and concentrated in vacuo to afford 18.1 g of a clear yellow liquid which by NMR was perfect for the desired product. The GCMS indicated the presence of both isomers.

Meta-chloroperbenzoic acid (mCPBA, 85%) was added portionwise to a solution of 2-((trimethylsilyl)oxy)-4-phenylbut-1-ene (8.8 g) in 300 mL of dichloromethane at 0° C. The temperature rose to 6° C. The reaction mixture was stirred in an ice bath for 30 minutes, then warmed to room temperature and stirred for an additional two hours. A white precipitate formed initially at low temperature but dissolved upon warming. After two hours at ambient temperature, the mixture was analyzed by GC which showed that all of the silylenol ether had reacted. GCMS showed an m/e of 236 for the desired enol ether epoxide.

The reaction mixture was washed with 100 mL of saturated sodium sulfite and twice with 100 mL of saturated sodium bicarbonate and concentrated in vacuo. The residue was dissolved in 40 mL of 1 M tetrabutyl ammonium fluoride in THF and stirred for 45 minutes. The was a slight exotherm. The reaction mixture was concentrated in vacuo then partitioned between 300 mL of methylene chloride and 100 mL of water. The methylene chloride layer was washed with 100 mL of saturated sodium bicarbonate, dried over sodium sulfate and concentrated in vacuo to afford 6.8 g of a brown oil.

GCMS and NMR of the brown oil indicated that both hydroxyketones had been formed although the 1-hydroxy was the major product. The crude oil was chromatograhped on a Biotage 40M using 4:1 hexane:ethyl acetate. The crude oil was loaded on the column with 10 mL of 1:1 ethyl acetate:hexanes. Fractions 9-11 contained the starting 4-phenyl-2-butanone. Fraction 20-24 contained ca. 0.3 g (4.6%) of 3-hydroxy-4-phenyl-2-butanone based on the NMR. Fractions 28-29 appeared to be cross contaminated with some of the 3-hydroxyketone by TLC so they were separately isolated to give 0.3 g of slightly impure 1-hydroxy-4-phenyl-2-butanone. Fractions 30-49 contained the pure product (1.6 g, 24%). The proton and carbon NMR spectra matched that expected for the desired product. The synthesis is summarized in Scheme I.

Example 35 Synthesis of S-(2-oxo-4-phenyl)butyl thioacetate

1-hydroxy-4-phenyl-2-butanone prepared as described above was dissolved in 10 mL of chloroform, cooled to 0-5° C. in an ice bath, then treated with 0.3 mL of thionyl chloride. The reaction was allowed to warm to room temperature and was stirred overnight at room temperature. The reaction mixture became dark and there was obvious gas evolution.

An aliquot was concentrated in vacuo and analyzed by NMR. The product had a spectrum consistent with the desired chloroketone. GCMS of the sample gave an m/e of 182 with the 3:1 chloride isotope ratio (182:184). The GC indicated that there was one major product. This material was used without further purification.

1-chloro-4-phenyl-2-butanone (about 0.44 g) was dissolved in 5 mL of DMF containing 0.2 mL thiolacetic acid. Triethylamine (0.4 mL) was added in a bolus and the resulting mixture was stirred at room temperature and monitored by GC and NMR. There was an exotherm and immediate salt precipitation. An aliquot was analyzed by GC and GCMS. The GC indicated a single new product and the GCMS showed an m/e of 222. The aliquot was also analyzed by NMR and found to be the desired product. The reaction mixture was filtered and the filtrate washed with 25 mL of ethyl acetate. The filtrate was partitioned between 25 mL of ethyl acetate and 15 mL of water. The ethyl acetate layer was washed with 15 mL each of 5% hydrochloric acid, saturated sodium bicarbonate and brine, dried over sodium sulfate and concentrated in vacuo to afford 0.4 g of a dark oil.

The oil was chromatographed on a Biotage 40S column using 1:1 chloroform:hexanes. Fraction 55 began to show product and at fraction 65 the elution solvent was changed to 60:40 chloroform:hexanes. Fractions 66:81 were combined and analyzed by NMR and GC and found to be about 50 mg of the desired product, S-(2-oxo-4-phenyl)butyl thioacetate, in 91% purity. Fractions 82-113 were combined and analyzed by GC and NMR and found to be 43 mg of the desired product in 95% purity. The synthesis is summarized in Scheme II.

Example 36 Synthesis of 5-phenyl-2,4-pentadienal

To a cooled (0-5° C.) 927 mL of 1 M solution of phenyl magnesium bromide in tetrahydrofuran was added dropwise a solution of crotonaldehyde (65.0 g) in 130 mL of anhydrous ether over a period of 2 hours and 45 minutes. The reaction was stirred for an additional 45 minutes and then warmed to room temperature. After four more hours of stiffing, saturated ammonium chloride aqueous solution (750 mL) was added to the reaction. The mixture was extracted with 750 mL of ether twice. The combined extract was dried over anhydrous potassium carbonate and filtered. The solvent was evaporated to give 135.88 g (99.9%) of the desired 1-phenyl-2-buten-1-ol as an oil which was used in the next step without further purification.

1-Phenyl-2-buten-1-ol (135.88 g) was dissolved in 2300 mL of dioxane and treated with 2750 mL of dilute hydrochloric acid (2.3 mL of concentrated hydrochloric acid in 2750 mL of water) at room temperature. The mixture was stirred overnight and then poured into 4333 mL of ether and neutralized with 2265 mL of saturated aqueous sodium bicarbonate. The aqueous phase was extracted with 1970 mL of ether. The combined extract was dried over anhydrous potassium carbonate. Evaporation of the solvent followed by Kugelrohr distillation at 30° C. for 30 minutes afforded 131.73 g (96.8%) of the desired 4-phenyl-3-buten-2-ol as an oil which was used in the next step without further purification. Dimethylformamide (DMF, anhydrous, 14 mL) was cooled to 0-5° C. and phosphorus oxychloride (8.2 mL) was added dropwise over a period of 40 minutes. The resulting solution was added dropwise to a cooled (0-5° C.) solution of 4-phenyl-3-buten-2-ol (10 g) in 32 mL of anhydrous DMF over a period of an hour. The reaction mixture was warmed to room temperature over a 35-minute period and then gradually heated up to 80° C. over a period of 45 minutes. The reaction was stirred at 80° C. for three hours and then cooled to 0-5° C. To the cooled reaction solution was added dropwise a solution of sodium acetate (40 g) in deionized water (100 mL) over a period of one hour. The mixture was then reheated to 80° C., stirred at 80° C. for an additional 10 minutes, cooled down to room temperature and extracted with ether (100 mL) twice. The combined extract was washed with brine (100 mL), dried over anhydrous sodium sulfate, filtered and concentrated under vacuum to yield 8.78 g of the desired 5-phenyl-2,4-pentadienal as a liquid which was used in the next step without further purification. ¹H NMR (CDCl₃, 300 MHz), δ(ppm) 7.51 (m, 2H), 7.37 (m, 3H), 7.26 (m, 1H), 7.01 (m, 2H), 6.26 (m, 1H). The synthesis is summarized in Scheme III.

Example 37 Synthesis of 5-phenoxy-2,4-pentadienal

2-Formylvinyl phenyl ether is prepared by treating phenoxyacetaldehyde with formaldehyde and diethylamine hydrochloride salt. The ether is then reacting with a solution of diethylphosphonoacetic acid and n-butyllithium in anhydrous tetrahydrofuran (THF) to form 5-phenoxy-2,4-pentadienoic acid. 5-Phenoxy-2,4-pentadienal is obtained by first converting the carboxylic acid to a Weinreb amide using oxalyl chloride followed by N,O-dimethylhydroxylamine. Subsequently, reduction of the Weinreb amide with lithium aluminum hydride (LAH) in THF leads to the formation of 5-phenoxy-2,4-pentadienal. The synthesis is summarized in Scheme IV:

Example 38 Synthesis of S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate

S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate is prepared as outlined in Scheme VA. 8-Phenyl-3,5,7-octatrien-2-one is made by reacting 5-phenyl-2,4-pentadienal in THF with an equal amount of acetic acid and piperidine followed by addition of acetone at room temperature under nitrogen. Treatment of 8-phenyl-3,5,7-octatrien-2-one with lithium diisopropylamide (LDA) and trimethylsilyl chloride (TMSCl) followed by m-chloroperbenzoic acid (mCPBA) leads to the formation of the alpha-keto alcohol. The alcohol is converted to the corresponding chloride by reacting with thionyl chloride. Subsequently, treatment of the resulting chloride with thiolacetic acid in the presence of triethylamine (TEA) give rise to S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate.

Alternatively, as shown in Scheme VI, S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate is made by converting 7-phenyl-2,4,6-heptatrienoic acid to the corresponding chloromethyl ketone by addition of oxalyl chloride dropwise in DMF followed by diazomethane and then treatment of HCl. The resulting chloromethyl ketone is treated with thiolacetic acid to form S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate.

Example 39 Synthesis of S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate

S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate is prepared in a similar manner, as shown in Scheme VB.

Example 40 Synthesis of 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one

1,1,1-Trifluoro-8-phenyl-3,5,7-octatrien-2-one is prepared as outlined in Scheme IIIA. 1,1,1-Trifluoro-8-phenyl-3,5,7-octatrien-2-one is prepared by reacting 5-phenyl-2,4-pentadienal in THF with an equal amount of acetic acid and piperidine followed by addition of 1,1,1-trifluoroacetone at room temperature under nitrogen.

Example 41 Synthesis of 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one

1,1,1-Trifluoro-8-phenoxy-3,5,7-octatrien-2-one is prepared in a similar manner, as shown in Scheme VIII.

Example 42 Synthesis of 1,2-epoxy-3-butanone

1,2-Epoxy-3-butanone was prepared by treating methyl vinyl ketone in methanol with 30% of hydrogen peroxide followed by 10% aqueous sodium hydroxide, as shown below.

Example 43 Synthesis of 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one

1-Oxiranyl-7-phenyl-2,4,6-heptatrien-1-one is made by dropwise addition of 5% aqueous sodium hydroxide to a mixture of 5-phenyl-2,4-pentadienal and 1,2-epoxy-3-butanone at a controlled pH of 8.5-9, as shown in Scheme X.

Alternatively, as shown in Scheme XI, 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one can be prepared by converting 7-phenyl-2,4,6-heptatrienoic acid to the corresponding Weinreb amide using oxalyl chloride followed by N,O-dimethylhydroxylamine. Subsequently, oxidation of the Weinreb amide with m-chloroperbenzoic acid (mCPBA) gives the desired alpha-keto epoxide.

Example 44 Synthesis of 1-Oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one

1-Oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one is made by dropwise addition of 5% aqueous sodium hydroxide to a mixture of 5-phenoxy-2,4-pentadienal and 1,2-epoxy-3-butanone at a controlled pH of 8.5-9, as shown in Scheme XII.

Assays

Compounds selected from ethylene glycol bisthioglycolate, ethyl 2-mercaptoacetate (each of which is commercially available from Sigma-Aldrich), S-(2-oxo-4-phenyl)butyl thioacetate, S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate, and S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate are used in the assays described below. Compounds selected from 1,1,1-trifluoro-5-phenyl-2-pentanone (prepared according to the procedure described in Biochim. Biophys. Acta (1999), 1420 (1-2), 45-56), 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one, and 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one are used in the assays described below. Compounds selected from 1-oxiranyl-8-phenyl-1-octanone (prepared according to the procedure described in Bioorg. & Med. Chem. Lett., 9 (1999), 2283-2288), 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one, or 1-oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one are used in the assays described below.

In Vitro Efficacy Studies—Extreme Drug Resistance (EDR) Assay

The PC3 cell line is maintained in RPMI supplemented with 10% fetal calf serum and antibiotics. Cells are suspended in 0.12% soft agar in complete medium and plated (2,000 cells per well) in different drug concentrations onto a 0.4% agarose underlayer in 24-well plates. Plating calls on agarose underlayers supports the proliferation only of the transformed cells, ensuring that the growth signal stems from the malignant component of the tumor.

All compounds are dissolved in DMSO to 200× stock solutions. Stock solutions are diluted to 20× working solutions using the tissue culture medium, then are serially diluted and added to the 24-well plates. The initial range of concentrations is 1 micromolar to 200 micromolar. No significant changes in pH of the culture medium are observed under the above conditions. Diluent control wells contain PC3 cells treated with DMSO, at the dilutions used for appropriate drug treatment. All experimental points are represented by two separate wells (duplicates). Four wells containing tumor cells that are not treated with drugs serve as negative controls in each experiment.

Cells are incubated with drugs under standard culture conditions for 5 days. Cultures are pulsed with tritiated thymidine (³H-TdR, New Life Science Products, Boston, Mass.) at 5 μCi per well for the last 48 hours of the culture period. Cell culture plates are then heated to 90° C. to liquefy the agarose, and cells are harvested onto glass fiber filters, which are then placed into counting vials containing liquid scintillation fluid. The radioactivity trapped on the filters is counted with a Beckman scintillation counter. The fraction of surviving cells is determined by comparing ³H-TdR incorporation in treated (experimental points) and untreated (negative control) wells. Microsoft Excel is used to organize the raw data on EDR experiments, and the SigmaPlot program is utilized to generate drug response curves. All drug response curves are approximated as sigmoidal equations (characteristic for typical drug response curves) to fit the data. IC₅₀ values are determined using the approximated sigmoidal curves and expressed as μM.

Histone (Hyper)Acetylation Assay

The effect of a compound described herein on histone acetylation can be evaluated in an assay using mouse erythroleukemia cells. Studies are performed with the DS19 mouse erythroleukemia cells maintained in RPMI 1640 medium with 25 mM HEPES buffer and 5% fetal calf serum. The cells are incubated at 37° C.

Histones are isolated from cells after incubation for periods of 2 and 24 hours. The cells are centrifuged for 5 minutes at 2000 rpm in the Sorvall SS34 rotor and washed once with phosphate buffered saline. The pellets are suspended in 10 mL lysis buffer (10 mM Tris, 50 mM sodium bisulfite, 1% Triton X-100, 10 mM magnesium chloride, 8.6% sucrose, pH 6.5) and homogenized with six strokes of a Teflon pestle. The solution is centrifuged and the pellet washed once with 5 mL of the lysis buffer and once with 5 mL 10 mM Tris, 13 mM EDTA, pH 7.4. The pellets are extracted with 2×1 mL 0.25 N HCl. Histones are precipitated from the combined extracts by the addition of 20 mL acetone and refrigeration overnight. The histones are pelleted by centrifuging at 5000 rpm for 20 minutes in the Sorvall SS34 rotor. The pellets are washed once with 5 mL acetone and protein concentration are quantitated by the Bradford procedure.

Separation of acetylated histones is usually performed with an acetic acid-urea polyacrylamide gel electrophoresis procedure. Resolution of acetylated H4 histones is achieved with 6.25 N urea and no detergent as originally described by Panyim and Chalkley, Arch. Biochem. Biophys. 130, 337-346 (1969). 25 μg Total histones are applied to a slab gel which is run at 20 mA. The run is continued for a further two hours after the Pyronin Y tracking dye has run off the gel. The gel is stained with Coomassie Blue R. The most rapidly migrating protein band is the unacetylated H4 histone followed by bands with 1, 2, 3 and 4 acetyl groups which can be quantitated by densitometry. The procedure for densitometry involves digital recording using the Alpha Imager 2000, enlargement of the image using the PHOTOSHOP program (Adobe Corp.) on a MACINTOSH computer (Apple Corp.), creation of a hard copy using a laser printer and densitometry by reflectance using the Shimadzu CS9000U densitometer. The percentage of H4 histone in the various acetylated states is expressed as a percentage of the total H4 histone.

The concentration of a compound required to decrease the unacetylated H4 histone by 50% (i.e., EC₅₀) can then be determined from data obtained using different concentrations of test compounds.

Histone Deacetylation Assay

The determination of the inhibition of histone deacetylase by compounds described herein is based upon the procedure described by Hoffmann et al., Nucleic Acids Res. 27, 2057-2058 (1999). The histone deacetylase is isolated from rat liver as previously described in Kolle, D. et al. Methods: A Companion to Methods in Enzymology 15: 323-331 (1998). Compounds are initially dissolved in either ethanol or in DMSO to provide a working stock solution. The synthetic substrate used in the assay is N-(4-methyl-7-coumarinyl)-N-α(tert-butyloxy-carbonyl)-N-Ω-acetyllysineamide (MAL).

The assay is performed in a final total volume of 120 μL consisting of 100 μL of 15 mM tris-HCl buffer at pH 7.9 and 0.25 mM EDTA, 10 mM NaCl, 10% glycerol, 10 mM mercaptoethanol and the enzyme. The assay is initiated upon the addition of 10 μL of a test compound followed by the addition of a fluorescent-labeled lysine substrate to each assay tube in an ice bath for 15 minutes. The tubes are transferred to a water bath at 37° C. for an additional 90 minutes.

An initial assay is performed to determine the range of activity of each test compound. The determination of IC₅₀ values is made from the results of five dilutions in range according to the expected potency for each test compound. Each assay is duplicated or triplicated.

Other Embodiments

From the above description, one skilled in the art can easily ascertain the essential characteristics of the present invention, and without departing from the spirit and scope thereof, can make various changes and modifications to adapt it to various usages and conditions. Thus, other embodiments are also within the claims. 

1. A method of treating spinal muscular atrophy in a mammal comprising administering to the mammal an effective amount of an inhibitor of histone deacetylase.
 2. The method of claim 1 wherein the inhibitor is a compound of formula (I):

wherein A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, or heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; or A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; each of the saturated and the unsaturated branched hydrocarbon chain being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; L is a straight C₂₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond; said hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; X¹ is O or S; and X² is —OR¹, —SR¹, —NR³—OR¹, —NR³—SR¹, —C(O)—OR¹, —CHR⁴—OR¹, —N═N—C(O)—N(R³)₂, or —O—CHR⁴—O—C(O)—R⁵, where each of R¹ and R², independently, is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group; R³ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group; R⁴ is hydrogen, alkyl, hydroxylalkyl, or haloalkyl; R⁵ is alkyl, hydroxylalkyl, or haloalkyl; and provided that when L is a C₂₋₃ hydrocarbon containing no double bonds and X² is —OR¹, Y¹ is not a bond and Y² is not a bond; or a pharmaceutically acceptable salt thereof.
 3. The method of claim 2, wherein the compound is 5-phenyl-2,4-pentadienoic acid, 3-methyl-5-phenyl-2,4-pentadienoic acid, 4-methyl-5-phenyl-2,4-pentadienoic acid, 4-chloro-5-phenyl-2,4-pentadienoic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoic acid, 5-(2-furyl)-2,4-pentadienoic acid, 5-phenyl-2-en-4-yn-pentanoic acid, 6-phenyl-3,5-hexadienoic acid, 7-phenyl-2,4,6-heptatrienoic acid, 8-phenyl-3,5,7-octatrienoic acid, potassium 2-oxo-6-phenyl-3,5-hexadienoate, potassium 2-oxo-8-phenyl-3,5,7-octatrienoate, cinnamoylhydroxamic acid, methyl-cinnamoylhydroxamic acid, 4-cyclohexanebutyroylhydroxamic acid, benzylthioglycoloylhydroxamic acid, 5-phenylpentanoylhydroxamic acid, 5-phenyl-2,4-pentadienoylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoylhydroxamic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid, 5-phenyl-2-en-4-yn-pentanoylhydroxamic acid, 5-(2-furyl)-2,4-pentadienoylhydroxamic acid, 6-phenylhexanoylhydroxamic acid, 6-phenyl-3,5-hexadienoylhydroxamic acid, N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid, 7-phenylheptanoylhydroxamic acid, 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid or 8-phenyloctanoylhydroxamic acid.
 4. The method of claim 2, wherein the compound is 5-phenyl-2,4-pentadienoic acid, 8-phenyl-3,5,7-octatrienoic acid, potassium 2-oxo-8-phenyl-3,5,7-octatrienoate, benzylthioglycoloylhydroxamic acid, 5-phenyl-2,4-pentadienoylhydroxamic acid, 6-phenylhexanoylhydroxamic acid, 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid, or 8-phenyloctanoylhydroxamic acid.
 5. The method of claim 1 wherein the inhibitor is a compound of formula (II):

wherein A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-14 membered heterocycloalkenyl, monocyclic aryl, or monocyclic heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; each of X¹ and X², independently, is O or S; Y¹ is —CH₂—, —O—, —S—, —N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —C(O)—O—, —O—C(O)—O—, or a bond; each of R^(a) and R^(b), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; Y² is —CH₂, —O—, —S—, —N(R^(c)), —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—, or —O—C(O)—O; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; L is (1) a saturated straight C₁₋₁₂ hydrocarbon chain substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, halo, carboxyl, amino, nitro, cyano, C₃₋₆ cycloalkyl, 3-6 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl, or at least two hydroxyl; and further optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; or (2) an unsaturated straight C₄₋₁₂ hydrocarbon chain containing at least two double bonds, at least one triple bond, or at least one double bond and one triple bond; said unsaturated hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, carboxyl, amino, nitro, cyano, C₃₋₆ cycloalkyl, 3-6 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(g))—, —N(R^(g))—C(O)—O—, —O—C(O)—N(R^(g))—, —N(R^(g))—C(O)—N(R^(h))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—; each of R^(g) and R^(h), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group; and R² is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group; or a pharmaceutically acceptable salt thereof.
 6. The method of claim 5, wherein the compound is benzylthioglycoloylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoyl hydroxamic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoyl hydroxamic acid, 5-phenyl-2-en-4-yn-pentanoyl hydroxamic acid, 5-(2-furyl)-2,4-pentadienoylhydroxamic acid, N-methyl-6-phenyl-3,5-hexadienoyl hydroxamic acid, or 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid.
 7. The method of claim 1 wherein the inhibitor is a compound of formula (III):

wherein A is a cyclic moiety selected from the group consisting of monocyclic aryl or monocyclic heteroaryl; each of said cyclic moieties being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, or amino; each of X¹ and X², independently, is O or S; each of R¹ and R², independently, is hydrogen, alkyl, hydroxylalkyl, or haloalkyl; each of R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹ and R¹⁰, independently, is hydrogen, C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, hydroxylC₁₋₄ alkyl, haloC_(h4) alkyl, or amino; and each of a, b, c, d, e, and f, independently, is 0 or 1; provided that at least one of b, c, d, and e is not zero; or a pharmaceutically acceptable salt thereof.
 8. The method of claim 1 wherein the inhibitor is a compound of formula (II):

wherein A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; each of the saturated and the unsaturated branched hydrocarbon chain being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; each of X¹ and X², independently, is O or S; each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c)), —N(R^(c))—C(O)—O—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; L is a saturated straight C₃₋₁₂ hydrocarbon or an unsaturated straight C₄₋₁₂ hydrocarbon chain, said hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, carboxyl, amino, nitro, cyano, C₃₋₆ cycloalkyl, 3-6 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further optionally interrupted by —O—, —N(R^(e)), —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, —O—C(O)—, —C(O)—O—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; R¹ is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, haloalkyl, or an amino protecting group; and R² is hydrogen, alkyl, hydroxylalkyl, haloalkyl, or a hydroxyl protecting group; or a pharmaceutically acceptable salt thereof.
 9. The method of claim 1 wherein the inhibitor is a compound of formula (IV):

wherein A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, and heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; or A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; each of the saturated and the unsaturated branched hydrocarbon chain being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; L is a straight C₃₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond; the hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; X¹ is O or S; and X² is —OR¹, —SR¹, or —SeR¹, wherein R¹ is hydrogen, alkyl, acyl, aryl or aralkyl; provided that when Y¹ is a bond and L is saturated, the carbon adjacent to Y¹ is not substituted with C₁₋₄ alkoxy or hydroxyl; or a pharmaceutically acceptable salt thereof.
 10. The method of claim 9, wherein the compound is S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate or S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate.
 11. The method of claim 1 wherein the inhibitor is a compound of formula (V):

wherein A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, and heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; L is a straight C₂₋₁₂ hydrocarbon chain containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond; the hydrocarbon chain being optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; and being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; X¹ is O or S; and X² is —OR¹, or —SR¹, wherein R¹ is hydrogen, alkyl, acyl, aryl or aralkyl; provided that when L is a C₂ hydrocarbon chain having at least one double bond, A is not C₃ cycloalkyl; or a pharmaceutically acceptable salt thereof.
 12. The method of claim 1 wherein the inhibitor is a compound of formula (VI):

wherein A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, and heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; or A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; each of the saturated and the unsaturated branched hydrocarbon chain being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; each of Y¹ and Y², independently, is —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —O—C(O)—O—, or a bond; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; L is a straight C₃₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond; the hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; and X¹ is O or S; X² is a halogen; provided that when Y¹ and Y² are each a bond, L is a C₆₋₁₂ hydrocarbon chain containing at least one double bond at C1, C2, C3 or C5 of the hydrocarbon chain from C═X¹, at least one triple bond, or at least one double bond and one triple bond, the hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C_(h) 4 alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; or a pharmaceutically acceptable salt thereof.
 13. A method of claim 12, wherein the compound is 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one or 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one.
 14. The method of claim 1 wherein the inhibitor is a compound of formula (VII):

wherein A is a cyclic moiety selected from the group consisting of C₃₋₁₄ cycloalkyl, 3-14 membered heterocycloalkyl, C₄₋₁₄ cycloalkenyl, 3-8 membered heterocycloalkenyl, aryl, and heteroaryl; the cyclic moiety being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; or A is a saturated branched C₃₋₁₂ hydrocarbon chain or an unsaturated branched C₃₋₁₂ hydrocarbon chain optionally interrupted by —O—, —S—, —N(R^(a))—, —C(O)—, —N(R^(a))—SO₂—, —SO₂—N(R^(a))—, —N(R^(a))—C(O)—O—, —O—C(O)—N(R^(a))—, —N(R^(a))—C(O)—N(R^(b))—, —O—C(O)—, —C(O)—O—, —O—SO₂—, —SO₂—O—, or —O—C(O)—O—, where each of R^(a) and R^(b), independently, is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; each of the saturated and the unsaturated branched hydrocarbon chain being optionally substituted with alkyl, alkenyl, alkynyl, alkoxy, hydroxyl, hydroxylalkyl, halo, haloalkyl, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, alkylcarbonyloxy, alkyloxycarbonyl, alkylcarbonyl, alkylsulfonylamino, aminosulfonyl, or alkylsulfonyl; each of Y¹ and Y², independently, is —CH₂—, —O—, —S—, —N(R^(c))—, —N(R^(c))—C(O)—O—, —N(R^(c))—C(O)—, —C(O)—N(R^(c))—, —O—C(O)—N(R^(c))—, —N(R^(c))—C(O)—N(R^(d))—, —C(O)—, —C(NR^(c))—, —O—C(O)—O—, or a bond; each of R^(c) and R^(d), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; L is a straight C₃₋₁₂ hydrocarbon chain optionally containing at least one double bond, at least one triple bond, or at least one double bond and one triple bond; the hydrocarbon chain being optionally substituted with C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ alkoxy, hydroxyl, halo, amino, thio, alkylthio, arylthio, aralkylthio, acylthio, nitro, cyano, C₃₋₅ cycloalkyl, 3-5 membered heterocycloalkyl, monocyclic aryl, 5-6 membered heteroaryl, C₁₋₄ alkylcarbonyloxy, C₁₋₄ alkyloxycarbonyl, C₁₋₄ alkylcarbonyl, or formyl; and further being optionally interrupted by —O—, —N(R^(e))—, —N(R^(e))—C(O)—O—, —O—C(O)—N(R^(e))—, —N(R^(e))—C(O)—N(R^(f))—, or —O—C(O)—O—; each of R^(e) and R^(f), independently, being hydrogen, alkyl, alkenyl, alkynyl, alkoxy, hydroxylalkyl, hydroxyl, or haloalkyl; X¹ is O or S; and each of R^(g), R^(h), and R^(i), independently, is hydrogen or C₁₋₆ alkyl; provided that when each of Y¹ and Y², independently, is a bond or CH₂, A is unsubstituted phenyl or heterocyclyl, and L is C₄₋₆, L has at least one double bond or at least one triple bond; or a pharmaceutically acceptable salt thereof.
 15. A method of claim 14, wherein the compound is 1-oxiranyl-8-phenyl-1-octanone, 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one, or 1-oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one.
 16. A method of treating spinal muscular atrophy in a mammal comprising administering to the mammal an effective amount of an inhibitor of histone deacetylase selected from the group consisting of: 5-phenyl-2,4-pentadienoic acid, 3-methyl-5-phenyl-2,4-pentadienoic acid, 4-methyl-5-phenyl-2,4-pentadienoic acid, 4-chloro-5-phenyl-2,4-pentadienoic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoic acid, 5-(2-furyl)-2,4-pentadienoic acid, 5-phenyl-2-en-4-yn-pentanoic acid, 6-phenyl-3,5-hexadienoic acid, 7-phenyl-2,4,6-heptatrienoic acid, 8-phenyl-3,5,7-octatrienoic acid, potassium 2-oxo-6-phenyl-3,5-hexadienoate, potassium 2-oxo-8-phenyl-3,5,7-octatrienoate, cinnamoylhydroxamic acid, methyl-cinnamoylhydroxamic acid, 4-cyclohexanebutyroylhydroxamic acid, benzylthioglycoloylhydroxamic acid, 5-phenylpentanoylhydroxamic acid, 5-phenyl-2,4-pentadienoylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoylhydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoylhydroxamic acid, 5-(4-dimethylaminophenyl)-2,4-pentadienoylhydroxamic acid, 5-phenyl-2-en-4-yn-pentanoylhydroxamic acid, 5-(2-furyl)-2,4-pentadienoylhydroxamic acid, 6-phenylhexanoylhydroxamic acid, 6-phenyl-3,5-hexadienoylhydroxamic acid, N-methyl-6-phenyl-3,5-hexadienoylhydroxamic acid, 7-phenylheptanoylhydroxamic acid, 7-phenyl-2,4,6-hepta-trienoylhydroxamic acid, 8-phenyloctanoylhydroxamic acid, benzylthioglycoloylhydroxamic acid, N-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 3-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-methyl-5-phenyl-2,4-pentadienoyl hydroxamic acid, 4-chloro-5-phenyl-2,4-pentadienoyl hydroxamic acid, S-(2-oxo-8-phenyl)-3,5,7-octatrienyl thioacetate, S-(2-oxo-8-phenoxy)-3,5,7-octatrienyl thioacetate, 1,1,1-trifluoro-8-phenyl-3,5,7-octatrien-2-one or 1,1,1-trifluoro-8-phenoxy-3,5,7-octatrien-2-one, 1-oxiranyl-8-phenyl-1-octanone, 1-oxiranyl-7-phenyl-2,4,6-heptatrien-1-one, and 1-oxiranyl-7-phenoxy-2,4,6-heptatrien-1-one.
 17. A method of treating spinal muscular atrophy in a mammal comprising administering to the mammal an effective amount of 7-phenyl-2,4,6-heptatrienoic acid. 